Peptidomic Analysis Reveals Seasonal Neuropeptide and Peptide Hormone Changes in the Hypothalamus and Pituitary of a Hibernating Mammal

Abstract

During the winter, hibernating mammals undergo extreme changes in physiology, which allow them to survive several months without access to food. These animals enter a state of torpor, which is characterized by decreased metabolism, near-freezing body temperatures, and a dramatically reduced heart rate. The neurochemical basis of this regulation is largely unknown. Based on prior evidence suggesting that the peptide-rich hypothalamus plays critical roles in hibernation, we hypothesized that changes in specific cell–cell signaling peptides (neuropeptides and peptide hormones) underlie physiological changes during torpor/arousal cycles. To test this hypothesis, we used a mass spectrometry-based peptidomics approach to examine seasonal changes of endogenous peptides that occur in the hypothalamus and pituitary of a model hibernating mammal, the thirteen-lined ground squirrel (Ictidomys tridecemlineatus). In the pituitary, we observed changes in several distinct peptide hormones as animals prepared for torpor in October, exited torpor in March, and progressed from spring (March) to fall (August). In the hypothalamus, we observed an overall increase in neuropeptides in October (pre-torpor), a decrease as the animal entered torpor, and an increase in a subset of neuropeptides during normothermic interbout arousals. Notable changes were observed for feeding regulatory peptides, opioid peptides, and several peptides without well-established functions. Overall, our study provides critical insight into changes in endogenous peptides in the hypothalamus and pituitary during mammalian hibernation that were not available from transcriptomic measurements. Understanding the molecular basis of the hibernation phenotype may pave the way for future efforts to employ hibernation-like strategies for organ preservation, combating obesity, and treatment of stroke.

Project and data background

We hypothesized that changes in cell–cell signaling peptides from the hypothalamus and pituitary may be responsible for regulating critical physiological changes during the hibernation season. To test this hypothesis, we applied a non-targeted liquid chromatography–mass spectrometry (LC–MS) and LC-tandem mass spectrometry (LC–MS/MS) “peptidomics” approach to identify and quantify endogenous neuropeptides and peptide hormones as a function of season and hibernation stage in the thirteen-lined ground squirrel. LC–MS and LC–MS/MS-based peptidomics allow the detection, identification, and quantification of peptides without preselection, allowing for findings not possible with targeted antibody-based methods.

Thirteen-lined ground squirrel hibernation cycle. A. Active thirteen-lined ground squirrel. B. Torpid thirteen-lined ground squirrel. C. Overview of the annual hibernation cycle and timeline for tissue sampling. The central circle represents months of the year progressing clockwise, with the general active period in white and the hibernation states of torpor and IBA in gray, as indicated in the center. Colored outer regions and text boxes indicate time points for sample collection for this study. For time points in pre-hibernation and hibernation seasons, the measured range of internal body temperatures is indicated in parentheses.

Pituitary

Label-free peptidomics

Total number of samples after LC-MS: 37

• August: 9

• October: 9

• IBA: 6

• Torpor: 5

• March: 8

Total number of feature provided: 124

Three step data processing:

• Batch correction

• Log2 transformation

• EigenMS normalization

Batch correction

Batch correction using package statTarget evaluates the missing values and a feature will be kept if it has non-zero value for at least 50% of samples (statTarget default is 80%) in any one group (remove 31 features). It then imputes missing values for the present features and QC-based signal correction. At last, it removes features CV% > 50% (default, removes 3 features).

Code

pheno <- "CNS_meta4samples_pituitary.csv"
dfile = "CNS_data4samples_pituitary.csv"
#labels <- read.csv("CNS_label4samples_pituitary.csv", row.names = "SampleName")

statTarget::shiftCor(pheno, dfile,  QCspan = 0.25, Frule = 0.5,
                     degree = 2,imputeM = "KNN", ntree=500, coCV = 50)

statTarget: Signal Correction Start... Time: Mon Nov 20 19:24:07 2023 

* Step 1: Data File Checking Start..., Time:  Mon Nov 20 19:24:07 2023 

 Data Link 
 metaFile: CNS_meta4samples_pituitary.csv 
 profileFile: CNS_data4samples_pituitary.csv 

 44 Meta Samples vs 44 Profile samples
 The Meta samples list (*NA, missing data from the Profile File)

 [1] "20220302_QC1" "20220302_QC2" "Pituitary_53" "Pituitary_31" "Pituitary_38"
 [6] "Pituitary_63" "Pituitary_55" "Pituitary_51" "Pituitary_50" "Pituitary_34"
[11] "Pituitary_59" "Pituitary_43" "20220302_QC3" "Pituitary_66" "Pituitary_26"
[16] "Pituitary_19" "Pituitary_24" "Pituitary_41" "Pituitary_57" "Pituitary_47"
[21] "Pituitary_52" "Pituitary_23" "20220303_QC1" "Pituitary_58" "Pituitary_44"
[26] "Pituitary_37" "Pituitary_39" "Pituitary_46" "Pituitary_65" "Pituitary_56"
[31] "Pituitary_48" "Pituitary_35" "Pituitary_61" "20220304_QC1" "Pituitary_49"
[36] "Pituitary_60" "Pituitary_54" "Pituitary_45" "Pituitary_42" "Pituitary_62"
[41] "Pituitary_25" "Pituitary_64" "20220305_QC1" "20220305_QC2"

 Meta-information: 

    Class No.
1  August   9
2     IBA   6
3   March   8
4 October   9
5      QC   7
6  Torpor   5
  Batch No.
1     1  44

 Metabolic profile information: 

               no.
QC and samples  44
Metabolites    128

* Step 2: Evaluation of Missing Value... 

 The number of missing value before QC based signal correction:  732
 The number of filtered variables using the modified  50 % rule :   31 

* Step 3: Imputation start... 

 The imputation method was set at 'KNN'
 The number of missing value after imputation:  0
 Imputation Finished! 
 
* Step 4: QC-based Signal Correction Start... Time:  Mon Nov 20 19:24:07 2023 

 The Signal Correction method was set at QC-RFSC 

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 Calculation of CV distribution of raw peaks (QC)...

        CV<5%   CV<10%   CV<15%  CV<20%   CV<25%   CV<30%   CV<35%  CV<40%
Batch_1     0 3.092784 22.68041 37.1134 54.63918 60.82474 69.07216 74.2268
Total       0 3.092784 22.68041 37.1134 54.63918 60.82474 69.07216 74.2268
          CV<45%   CV<50%   CV<55%   CV<60%   CV<65%   CV<70% CV<75% CV<80%
Batch_1 77.31959 87.62887 91.75258 94.84536 95.87629 98.96907    100    100
Total   77.31959 87.62887 91.75258 94.84536 95.87629 98.96907    100    100
        CV<85% CV<90% CV<95% CV<100%
Batch_1    100    100    100     100
Total      100    100    100     100

 Calculation of CV distribution of corrected peaks (QC)...

           CV<5%   CV<10%   CV<15%   CV<20%   CV<25%  CV<30%   CV<35%   CV<40%
Batch_1 1.030928 20.61856 41.23711 59.79381 68.04124 74.2268 82.47423 90.72165
Total   1.030928 20.61856 41.23711 59.79381 68.04124 74.2268 82.47423 90.72165
          CV<45%   CV<50%   CV<55% CV<60% CV<65% CV<70% CV<75% CV<80% CV<85%
Batch_1 92.78351 96.90722 98.96907    100    100    100    100    100    100
Total   92.78351 96.90722 98.96907    100    100    100    100    100    100
        CV<90% CV<95% CV<100%
Batch_1    100    100     100
Total      100    100     100

* Step 5:  Removal of the features (CV% > 50%) Mon Nov 20 19:24:08 2023 

 No. of removed features: 3
 Feature name: LAGAPEPAEP KRLGVLFNPYYDPLQWKSSRFE TPEAQAAFQKVVAGVANALSHKYH 

 Output Link: C:/Users/qiuha/OneDrive/projects/MaxHub/projects/2023-07-03-CNS-groundsquirrel 

 Correction Finished! Time:  Mon Nov 20 19:24:08 2023 

 #################################### 
 # Software Version: statTarget 2.0 + # 
 # Email: luanhm@sustech.edu.cn# 
 #################################### 

Code

fh = read.csv(file = "statTarget/shiftCor/After_shiftCor/shift_sample_cor.csv",header = TRUE, row.names = 1, stringsAsFactors = FALSE, sep = ",") %>%
        t(.) %>%
        as.data.frame()
labels_d1 <- as.matrix(fh[1,])
N_feature = nrow(fh[-1,])

# change row annotation for heatmap
fh_mod = read.csv(file = "statTarget/shiftCor/After_shiftCor/shift_sample_cor_mod_pituitary.csv",header = TRUE, row.names = 1, stringsAsFactors = FALSE, sep = ",") %>%
        t(.) %>%
        as.data.frame()

feature_name = as.matrix(fh_mod[-1, "sample"]) %>%
        `rownames<-`(rownames(fh_mod)[-1]) %>%
        `colnames<-`("name") %>%
        as.data.frame() %>%
        rownames_to_column(., var = "variable")

• Features = 94

Data preview (after batch correction)

Code

#rownames(fh)[-1] == feature_name$variable
rownames(fh)[-1] = feature_name$name
# display table
fh %>% 
        #mutate(across(-variable, round, digit=2)) %>%
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

	Pituitary_53	Pituitary_31	Pituitary_38	Pituitary_63	Pituitary_55	Pituitary_51	Pituitary_50	Pituitary_34	Pituitary_59	Pituitary_43	Pituitary_66	Pituitary_26	Pituitary_19	Pituitary_24	Pituitary_41	Pituitary_57	Pituitary_47	Pituitary_52	Pituitary_23	Pituitary_58	Pituitary_44	Pituitary_37	Pituitary_39	Pituitary_46	Pituitary_65	Pituitary_56	Pituitary_48	Pituitary_35	Pituitary_61	Pituitary_49	Pituitary_60	Pituitary_54	Pituitary_45	Pituitary_42	Pituitary_62	Pituitary_25	Pituitary_64
class	August	Torpor	IBA	October	August	August	August	Torpor	October	March	October	Torpor	Torpor	Torpor	March	August	March	August	IBA	October	March	IBA	IBA	March	October	August	March	IBA	October	August	October	August	March	March	October	IBA	October
AGAPEPAEPMELAKPSA	8440.891791	775.554963	894.443289	11.425360	1548.747707	16807.763410	7436.475845	24.346540	1116.529464	4772.051234	477.122095	1347.690917	4.423521	779.355400	5978.243266	14785.218490	1030.061559	1617.177966	963.767877	26.824983	4079.207738	1310.612505	1056.466008	1104.657872	109.499447	475.793453	1154.425233	1146.309064	952.829079	6014.112942	728.606820	6652.094453	40.168600	45.421386	133.549590	1696.183331	980.962340
LAGAPEPA	1637.378702	575.595032	975.630047	45.861858	618.251226	6120.353519	5723.721568	99.165909	48.814586	1434.796982	125.069634	8881.278769	163.538557	227.448079	872.068168	8555.658726	130.762483	1051.025765	15.254078	69.059286	2.970965	4940.096814	33.457682	40.529443	64.864598	2213.437898	82.727210	2029.214809	201.302627	5663.122020	55.439455	4929.551350	91.342434	73.612294	253.726328	5986.048232	218.966671
AFGPRGPGLQL	550.29629	649.65194	755.18678	345.80726	1221.06916	791.64920	881.68783	812.51054	20.84877	2777.31318	356.64258	456.75401	801.66424	688.52076	804.50951	548.14269	590.88412	333.61744	475.63361	624.53244	1184.96964	565.58643	362.17408	2421.97165	4249.72287	478.94991	1558.92600	1171.09202	2395.91454	1019.61708	2884.94196	2131.58046	1049.11926	453.65046	596.25238	180.22440	826.22788
AAMDLEL	525.06319	13.00213	874.75070	1218.98064	7439.16463	25.49921	297.86676	924.28122	689.19719	375.21130	629.74732	124.37370	784.78327	957.32957	2253.14606	671.64965	449.49625	303.24242	1481.36860	829.00897	611.15013	675.69158	736.71143	1012.66076	22.83013	952.48399	416.59759	57.17709	442.89607	552.91798	4101.33316	1482.06788	482.06852	814.28190	1113.41676	116.09223	137.89368
AELDQLLHY	1521.42903	1002.28099	319.04781	1904.33387	2971.66541	2247.60675	72.35338	1899.71042	2508.03824	4280.23291	3344.65898	858.16806	2704.74526	157.78970	796.25832	5154.79758	665.90566	331.78645	4495.39135	1127.25751	2517.78311	2150.77456	234.06884	3391.50560	1430.31875	360.19220	745.14195	244.52844	212.58989	1280.93174	706.79407	947.91799	2080.38023	1587.68654	613.10502	795.80551	718.56146
EDREEASLQDRQYASHHT	42.17504	797.29683	1235.93663	645.17823	184.07864	547.59149	489.51312	1215.11341	1156.37250	2059.00835	1077.36160	1069.12980	382.01498	980.73374	247.32133	586.13359	1602.37731	665.29413	1551.51409	172.45288	2739.57538	257.36413	1022.67087	2859.40863	697.95067	710.02483	364.97251	1410.20775	1408.38193	385.27649	767.71181	135.72669	703.49989	707.01072	632.72335	446.80660	519.89247
EDREEASLQDRQYASHHTTE	103.494268	527.248428	902.432299	530.758483	213.092060	538.638119	498.095470	977.873970	800.188114	1931.523871	531.038140	765.766642	414.387373	1069.247181	562.047648	645.154991	1606.570019	673.070093	1508.743502	235.332843	2955.934267	252.633601	1234.983948	4391.329206	679.960741	666.583467	662.772621	1163.094189	1411.795110	497.315730	1398.673698	307.393847	818.341676	207.556735	2.944484	534.580232	1040.775925
EEASLQDRQYASHHT	55.977706	577.709867	1326.664190	835.710334	55.430721	403.754716	396.416524	1575.441576	1555.499722	1816.940059	1266.284003	1069.694237	416.330001	941.406267	183.235430	222.398505	1248.631166	519.670512	1470.596814	252.783118	2282.001923	248.859735	1279.058948	2761.773044	1049.763295	208.921965	406.380606	1545.591591	1714.273409	102.133829	990.366681	71.689021	441.925256	110.825801	4.302888	505.348092	725.029992
EEASLQDRQYASHHTTE	139.71983	495.46860	1072.65147	572.76324	217.54310	527.15196	549.87897	1318.03658	940.23415	1734.41444	650.58705	787.96181	481.14419	988.25398	436.81115	623.64710	1790.77073	630.12132	1380.09498	267.59218	2384.29342	310.02315	1187.27888	3739.72553	1056.69198	580.88166	690.62213	1345.06364	2049.28193	368.99512	1596.60559	342.84747	566.92150	136.15521	25.30894	501.69637	1215.65739
EESEESEEGTTSEVT	254.28797	396.82302	1454.76710	524.26478	459.59644	223.76097	445.93341	2431.03205	803.17354	370.86905	1407.42960	397.53098	1538.47669	8100.06053	118.40360	403.21272	2990.34082	412.19670	2156.28479	1791.83580	2406.82879	323.59815	1303.54333	2270.37937	2172.79854	148.13757	283.37044	2946.79497	2340.76900	521.42110	2066.92534	424.30620	365.28014	65.94815	2086.61914	760.79018	987.37709
ELDQLLHY	1029.73311	1510.97697	1067.39391	669.81819	983.48923	628.20442	681.85894	1020.06360	1299.43517	1795.94991	1401.02161	460.30632	2154.10252	801.67790	1359.26169	856.45478	1468.28770	319.17416	1340.78192	788.31253	1803.85903	552.30906	790.46238	3595.49952	2729.17864	301.69341	2465.12908	1420.89800	1957.30849	97.86531	992.35921	417.34480	593.74461	32.96241	915.30199	194.77194	1188.81152
FLGEAYHHVPE	493.4311	322.7630	657.7509	369.3847	734.5341	629.2542	320.0933	677.0220	115.5980	2320.1347	374.6594	439.0358	949.0371	444.6169	1248.6644	1500.9906	300.2621	131.0724	1904.5890	1034.1041	670.1074	2005.1242	255.0434	1771.6900	1546.4188	127.9063	471.0338	291.5775	496.3285	612.4399	453.2683	162.8636	1206.0531	1271.5075	23.3822	1071.1865	326.5323
FLGEAYHHVPES	481.21481	654.24171	1047.65011	329.80621	842.32271	515.26592	682.86542	1326.22183	225.60144	2239.06766	721.41903	694.97339	1288.01876	504.01045	525.07038	528.91362	841.68651	1096.58151	1512.49735	1144.77095	954.72033	1152.73119	258.74070	1417.68697	1635.10268	72.67321	628.49496	643.30132	2065.45078	441.04958	787.10100	206.27630	957.96976	128.69579	213.47122	515.66261	285.22421
FLGEAYHHVPESQ	428.70360	758.26145	912.96618	406.40473	846.08793	79.05816	783.88383	1395.71003	249.02890	2313.96918	465.60644	809.88547	809.16139	749.01573	464.38649	554.87005	890.71067	299.68694	1294.83834	919.60470	841.72658	593.31631	185.36898	2804.12490	1713.15637	153.82720	1060.05182	1188.88783	2069.10972	84.42699	803.96634	495.43250	994.35460	367.69513	267.12389	564.01480	505.96548
FLGEAYHHVPESQRD	247.7085	488.8710	753.6601	482.4274	675.5019	372.5328	446.2955	883.9051	223.1465	2342.6750	325.4790	343.9048	700.3629	781.2719	1024.8392	527.7075	1813.8460	450.1383	1419.6284	851.5824	1643.1506	599.7167	362.1726	5741.6535	1112.5673	210.4716	2430.3198	963.9576	1414.9978	564.0439	1589.6277	677.4201	1246.0614	687.5427	20.1341	443.1950	530.4494
FLGEAYHHVPESQRDKA	63.83861	425.14360	708.01010	691.15817	345.96203	410.27961	421.94871	834.57931	232.34500	2402.56414	180.76880	548.61649	472.53191	820.97403	962.28249	745.17544	1806.78991	262.12347	1347.75389	681.88412	1137.75698	1544.45893	672.18398	5446.53105	645.23605	201.77124	1564.56968	609.19995	1340.20771	585.85442	2231.79484	614.44507	2304.55415	305.02820	949.50425	754.30831	762.21780
GEAYHHVPESQRD	108.5881	662.3954	1698.3930	352.3198	189.7030	106.8252	472.2040	1208.0028	446.6579	2028.1897	909.4631	782.0409	1480.9752	1081.6284	1589.6561	1685.8281	911.1899	160.9587	1582.7503	427.2400	1697.3173	1132.9635	1480.3471	3353.7126	987.9464	314.1462	894.3933	1224.2174	1607.2474	341.8750	2879.8256	530.0516	524.4536	330.8959	743.9444	876.1253	804.6718
GEAYHHVPESQRDKA	11.92236	395.62409	813.88227	501.06086	239.91843	400.09200	253.31832	734.02854	386.50858	1920.88127	174.43463	1008.40384	987.85891	684.55000	1872.89073	1242.10266	1235.12391	114.96755	1106.49652	428.55056	995.45208	2367.28765	2066.11269	4548.26675	720.33087	120.43822	805.45484	311.28189	1244.85174	432.56575	3258.74429	327.14693	1474.92964	251.63912	925.21924	457.54335	567.04523
GVLFNPYYDPLQWKSSRFE	6611.4346	875.9025	685.7050	472.3530	865.2550	1074.7683	3886.0569	331.1997	960.9155	7846.9287	543.5063	2637.2926	1005.2123	218.1399	1472.0790	6479.8435	1142.6181	203.2473	1050.6886	394.2170	1674.5674	2205.6678	960.0407	4358.9356	985.1988	1677.7208	2466.2344	881.2165	4798.2964	1318.4202	1715.2404	11978.9482	471.7387	2172.5147	1197.1231	1155.3646	1948.9287
LDQLLHY	275.9542	793.0110	895.8305	451.5764	1004.0843	279.7714	288.4017	1994.8197	932.9811	3206.3428	544.0862	219.0557	2486.7365	749.9878	1264.3156	621.4381	1052.6288	534.3379	1757.2866	1132.4615	2160.3010	1447.9382	865.8969	3079.2076	1420.9880	163.3341	1491.3648	724.8362	846.6669	262.0112	1123.4937	387.9258	1457.3647	1070.4640	1303.5664	455.8696	751.2653
LGEAYHHVPESQRD	167.21461	550.89299	761.28101	416.57572	664.14201	43.32686	192.79973	947.61855	127.53569	3021.89913	167.23181	190.43521	841.13448	878.00125	954.61050	721.53158	1938.28268	257.33678	1739.43515	878.69710	1862.44146	827.99034	184.08044	5794.52841	1276.08095	86.16034	2340.22125	730.11514	1150.07058	346.23813	1836.12807	822.88674	2173.45214	518.13479	738.44704	487.49897	39.91444
LGVLFNPYYDPLQWKSSRFE	8669.6495	627.6412	657.2180	2093.6500	4464.1618	2311.5561	10826.9857	1080.3823	1941.9735	9129.7677	1663.8509	2553.1065	417.4635	312.6697	442.5947	12800.4487	730.3036	806.9694	1341.2673	835.1249	3117.1786	2264.1320	176.6967	11557.5027	2057.3074	4560.8705	4188.6763	2091.2422	5271.7920	7873.1617	5597.6518	16651.9515	1866.7894	1832.6857	1731.6016	509.6936	1664.2611
Q(-17.03)KIAEKFSQ	394.65207	989.09485	1563.36256	174.54546	76.71573	631.76771	10.75832	2022.87482	332.67193	793.28098	239.85917	236.07875	396.79905	2330.69967	864.55441	241.44595	794.72469	581.56294	1167.23519	1036.85109	964.04812	412.62181	1028.77867	1979.95156	1382.01711	345.09604	1434.80009	298.36758	2180.02907	367.47702	2715.75645	74.14704	769.91394	125.13626	888.36737	313.74587	99.00356
Q(-17.03)KIAEKFSQR(-.98)	13.555279	412.189102	857.423054	63.616254	38.934850	530.182135	5.441377	1219.043920	366.004642	704.230341	77.965252	315.974786	418.366163	1271.987762	1415.228254	444.460457	1853.511233	230.219022	1428.640272	1358.385843	2389.541328	752.584749	1658.803085	3418.286575	1078.201212	706.032686	1213.248992	202.746358	896.524996	731.196235	3804.701044	120.987800	1791.039468	406.218462	311.066852	624.413222	103.382018
Q(-17.03)YDRVAELDQLLHY	16423.77064	220.46894	324.73862	3250.03108	3600.84988	3194.66819	13497.81109	854.97455	2641.47061	8033.12524	2085.40169	1450.06221	386.99210	271.41982	898.83112	15508.98794	849.99339	310.55343	840.38469	908.70988	2369.15980	2064.59586	46.19556	4049.32491	4933.21084	3718.76707	3083.31826	673.65307	3248.15809	5186.08688	4082.30745	33985.28329	3112.48130	4548.34755	95.67132	659.50459	567.47456
QYDRVAELDQLLHY	1779.169075	110.810896	1984.625763	3073.594982	4481.431768	1519.311376	2896.246777	1735.430427	2199.744258	3831.964478	3092.654594	548.393817	703.703883	504.263075	1197.232466	2186.854596	380.145695	372.932879	1400.544479	606.524804	4054.252621	1498.332456	383.825462	4.910719	2056.050241	1195.321366	578.218830	1101.266090	1118.642384	1406.298599	1456.922656	6738.520580	2090.537237	1501.578752	60.034898	425.761408	1175.979262
RVLTEEEEKELENL	1496.1039	1489.5749	1863.2634	425.9575	1257.1078	4316.7888	1761.4553	3408.0382	1564.9475	1699.1262	884.2519	553.1472	803.3353	3182.5054	2451.1502	1203.1286	362.0642	271.8096	5294.0775	4540.5105	1756.6278	1046.7054	1467.0762	1164.8802	1742.0443	1118.4210	1500.4058	1210.1720	3468.4995	2327.7286	10675.1755	408.1506	1036.4430	686.7855	126.4312	660.8108	225.2719
SQGGEPGAYLTPDT	933.8392	1007.3850	902.4255	354.2801	965.4500	302.4190	470.7034	875.1652	573.3923	1174.4731	320.0198	857.8360	878.6701	642.4561	959.2307	394.1289	1324.9163	692.6524	1408.6957	472.0319	937.2687	696.1563	500.3454	3518.6506	1927.9244	142.7497	391.3537	774.4224	1072.9653	410.5230	1002.5809	773.8843	627.6872	299.4090	568.1871	517.6635	1022.8996
SQGGEPGAYLTPDTREE	457.2856	436.5969	630.6995	330.7102	1144.8602	462.1013	501.0232	494.7017	579.0398	1321.0060	389.4226	565.9996	897.9201	861.9230	621.8995	617.8421	1222.0180	673.9228	1294.0884	1031.7024	769.4819	487.2670	506.1190	1807.9632	798.6428	182.9074	1293.4814	440.0699	730.5911	519.7184	907.3238	591.6321	688.3643	319.6933	894.5599	385.4963	774.6026
SSQEGNPPSEERGHTLQEPEEAKVGE	270.4985	730.6174	615.5500	436.6446	1081.0976	975.8356	1258.7788	1002.5869	569.9957	1896.9526	492.3425	1096.8643	638.1843	1216.7679	690.9403	1828.5668	1834.4817	762.8766	2071.3178	582.5196	2029.7862	853.9988	583.4784	3717.7003	2620.9343	788.7831	1875.7158	1705.9751	1000.8422	1656.7842	940.2866	1263.6121	2044.5158	190.9979	187.9178	1690.1970	929.7172
VAELDQLLHY	710.6329	1661.2074	995.6014	2024.5493	3404.2238	1685.2024	1091.5948	1560.6975	1872.9170	137.2283	1753.6776	503.8729	1332.1929	549.8334	1522.4090	1996.1246	540.6041	499.3167	2132.7675	989.0957	2696.9916	1340.7765	367.5124	5604.4396	1701.2064	644.0655	1015.1564	1223.6588	1170.9386	1159.5714	1486.2551	2652.1020	1270.3575	1139.8518	1164.6195	225.5111	539.7864
YDRVAELDQLLHY	1921.2349	779.4586	1183.3663	4642.7824	5231.8957	2200.0387	1612.0324	1169.5422	3437.6512	3720.9585	4187.5864	612.2748	571.2310	169.8196	2095.6228	8518.2837	193.6967	124.2603	2001.3383	1399.9847	4114.0251	3023.2594	116.8445	1047.7075	3320.1231	1317.3165	406.6363	125.3643	536.7377	3125.2496	1696.5310	7766.6467	3266.3952	4275.8072	1328.8320	866.0230	740.5959
Q(-17.03)EPGAPAAGM	1182.6064	576.3984	776.1936	614.1799	1189.9451	2163.6382	1409.6190	809.8199	537.4106	1427.3021	551.5436	765.6882	685.3389	691.1032	868.2769	1018.9770	1526.9570	1232.3924	1170.6636	871.0869	1397.0738	767.7241	608.4399	1653.6092	2759.6232	433.5372	148.7911	2045.6867	2017.5743	2077.3394	2125.9028	1808.6240	1003.3029	707.0681	1967.4411	649.9396	1036.2081
SLDSPAGPA	1407.60227	597.20486	899.90567	599.69070	876.35173	1004.43049	1218.87335	92.19355	1193.21654	744.44072	564.87617	814.56617	647.64301	167.62533	62.61696	1110.08840	4962.65211	2782.84682	60.08567	216.29559	1330.02735	729.76293	1297.97498	3689.57339	6127.75839	692.13749	6119.97577	5076.68455	1459.45084	451.28754	2567.89114	442.38150	1960.05130	56.60028	956.03057	2475.50683	3288.53589
SLDSPAGPAE	224.688672	776.741851	1139.862167	323.229867	785.439721	229.639017	1063.428607	110.943635	1542.458008	368.718257	434.823797	921.740524	389.621240	341.448954	39.152612	6.308664	5868.176667	2822.689795	6.518965	128.809849	779.917445	721.876138	1145.982574	3966.032611	4610.137183	168.784033	6080.818746	2725.968495	1275.506683	195.326074	1657.595108	164.686308	2047.773879	235.508453	5.756192	1898.797220	2854.147910
VKVGVNGF	2212.1589	879.3813	312.4563	1385.2188	4011.5349	2161.7012	354.8655	307.8283	2990.9895	735.4303	721.8823	1468.7655	541.6038	467.4043	2533.7810	728.5705	1485.0691	121.0391	897.2713	890.5916	1422.0956	1996.4345	787.9567	2124.6160	8452.9563	1242.5262	1293.7715	212.3951	314.7743	756.8240	293.1550	1231.0724	2685.2269	4635.4415	1491.9776	1439.5450	945.5468
Q(-17.03)HWSYGLRPG(-.98)	821.423755	887.395308	543.252364	573.822647	896.330038	156.486655	1322.969829	336.261309	271.589693	1232.051280	749.754688	55.270095	778.814142	349.856089	132.108752	89.240132	2185.141985	2174.950579	64.780758	326.457993	1046.780803	271.666059	7.128048	1345.333136	1344.761419	558.409425	2109.564757	1479.411528	2179.336941	608.336491	1081.103300	174.328387	1556.556669	994.782829	33.617020	544.336962	529.181934
SVSTVLTSKYR	511.74364	1066.83668	629.23461	630.64485	3291.97912	2792.32956	194.22572	502.86604	1242.77294	843.25636	742.65424	1058.82814	245.98463	877.25843	579.91026	329.10116	1844.81809	81.93880	1037.88314	2626.49562	815.30701	1796.57417	713.04349	1496.32049	2738.00545	385.33324	856.21166	73.93288	148.02640	1169.23286	597.59938	832.91949	1969.21699	1570.60247	1803.43038	1538.27855	1226.10399
GVANALSHKYH	84.97186	1420.81691	714.41442	1198.17922	1798.47488	473.04146	230.27930	859.93232	2164.51731	1565.97138	1204.75999	820.22776	218.86975	1253.04894	836.43356	1065.06708	4211.75240	83.51805	1722.24996	1795.43793	1781.37783	2311.58571	72.17162	2251.25115	2241.27363	1538.07529	61.26901	476.15935	116.28334	1298.83855	158.88758	911.07471	2812.79265	2195.76618	60.91228	19.43212	1171.83679
KVVAGVANALSHKYH	1295.3962	1228.5311	519.0045	855.6822	2369.9914	1028.9242	221.7337	476.4842	1179.8338	1920.9000	797.2765	925.3959	1419.1548	1188.2542	1135.3516	1072.8624	4026.0229	1482.9382	2048.9855	1439.2888	2041.0056	2698.7278	1232.3757	2661.1546	2109.3469	1183.9586	1319.4228	377.8791	1695.2464	2227.9271	1706.0109	1186.8453	3442.8773	2827.0645	1501.2990	1312.7818	968.7908
VANALSHKYH	67.77349	1510.54698	825.89552	2233.12137	901.70499	350.61214	348.92269	887.73587	4385.58244	1105.96771	2140.00307	690.91956	286.35218	1264.09210	840.82224	1769.60580	2323.03594	49.58380	894.60897	811.80865	1662.20278	3205.02220	57.44170	1938.65977	1856.28805	2007.90450	1601.26430	317.38474	53.90293	1569.80784	192.17078	1132.54046	1147.00757	1722.93609	64.90289	934.87208	1522.23353
GRTLYGFGG	210.79106	1047.61329	292.41303	1247.20614	2161.54613	2053.18357	245.41516	636.79697	1765.78190	168.56984	1112.69824	117.12027	732.53098	781.40538	1745.69030	395.69164	2406.19717	349.26655	1260.23134	1421.68460	1503.41041	1741.02772	127.54586	1569.82459	6212.41099	455.63762	262.09716	609.21820	587.59834	846.15612	400.16026	955.21457	3212.91745	1672.19179	1510.66823	96.54891	56.25776
RTLYGFGG	223.6174	978.2271	220.2125	1533.7512	2525.2230	1701.0789	174.2894	557.3945	2168.6592	301.2160	1100.3548	119.3319	641.3648	791.2343	1525.5741	331.1254	2565.5384	322.1529	1092.1647	1331.8070	1327.8681	1812.3511	191.5573	1191.3973	7186.2700	550.2879	283.0906	614.8341	626.6266	576.0633	562.7893	746.3481	3190.7879	2513.4609	1604.2847	148.7276	113.1286
TLYGFGG	1078.42158	2632.59413	1322.19361	2237.88478	4281.83058	2700.18873	3833.76464	228.52010	2696.80900	433.17355	2303.16981	36.58765	5557.08767	219.91817	1941.22982	825.04401	902.70937	3843.43252	449.70379	408.15663	505.09863	1527.71901	1161.16800	872.80191	5251.73941	509.61539	4088.48295	1983.02510	2220.11131	319.16476	991.16706	502.27567	1601.03847	3974.15696	375.33475	562.29194	1314.31080
AADQDLGPEAPPEGVLGA	2901.8157	672.7262	177.7539	358.4347	1313.7772	1262.3843	4857.9957	1052.5964	763.6487	3256.6101	755.3845	1450.1382	495.3376	116.4219	1540.4689	1655.2416	771.4656	174.7108	459.6791	491.2544	816.9146	1326.2971	518.6031	918.1944	1280.8434	1068.5097	2000.2317	1555.2968	840.4997	2130.0988	450.0622	3194.4151	1136.8468	230.8847	1079.4181	1843.1214	2223.0568
AADQDLGPEAPPEGVLGAL	20153.3480	956.6158	204.6107	6386.2001	8540.2739	3845.5771	22177.9979	2953.2585	3032.4969	15476.4061	2385.2506	2401.1125	164.0238	557.3158	2009.3125	9596.4939	827.6753	981.9257	997.2533	290.5575	3928.4518	1742.7590	1025.8917	5205.2513	8052.2519	6171.2306	3032.4938	1175.8996	2206.6297	8989.4532	939.2032	36212.0728	3388.6153	10166.8262	885.1045	2434.9761	2690.4065
LENPQPQAPARRLLPP	1190.76922	842.61542	439.98537	491.07796	930.34859	801.49427	1392.92750	188.72075	137.78095	977.42039	739.44097	977.16104	916.94428	422.38212	825.49809	780.67822	836.42948	1571.69028	262.91801	475.12640	781.69005	818.23824	206.25306	1274.53917	3190.16541	828.48681	1070.73824	1148.82049	1426.29262	2312.41875	1083.13822	781.48364	1992.09689	493.57180	34.18693	1305.72102	627.64834
VKMALQQEGFD	1433.4862	827.2746	407.0671	238.9144	2355.4541	5705.0479	2638.0575	629.5865	1136.9658	783.1829	257.5033	1726.0843	621.0280	334.7879	1295.9967	1052.0031	1172.2126	1299.0673	504.1724	721.1416	730.3526	1022.2065	388.7564	396.4622	3675.0981	1000.5473	842.4559	1938.2006	1100.3952	4473.3412	579.8407	1830.7952	1325.4213	370.3733	385.7423	880.4956	217.6216
GGFMRGL	1496.46263	1688.20867	591.83332	1498.25623	496.09793	177.63674	542.55803	1035.70028	934.90147	767.92367	1078.73139	1587.19706	5060.28470	90.51220	133.56343	253.05359	835.96457	2446.87459	656.92193	467.99198	792.96502	3460.92931	70.88582	1551.98913	4250.68241	589.34582	1106.41402	2006.17226	114.91533	648.92810	669.08974	883.41027	4533.29436	2048.69724	1950.28559	1273.68088	839.50276
Q(-17.03)LEDEAKELQ	775.99320	1479.36541	710.35774	459.31607	1647.03835	818.38893	161.52018	148.02224	306.23259	1303.45631	909.55371	1257.71787	1962.34358	213.01920	1692.68030	210.58887	2057.22799	4083.38718	177.80203	413.99111	1572.62460	1326.20146	1193.50844	1279.52295	5273.62608	767.82309	2320.95430	2982.26184	1476.29250	1064.10736	1366.63939	729.70625	1780.75972	578.13398	91.66786	1705.47619	4848.67783
SPQLEDE	276.940288	1396.146722	868.421715	1621.192868	541.077833	157.469711	1376.129368	173.778454	536.193917	599.786281	2129.672108	3.747196	2007.199859	182.917465	1630.921342	151.337529	2475.792186	3013.991442	168.921508	344.846822	977.798290	1594.029523	1164.211456	2069.255579	7458.458534	1465.719104	2979.703605	5069.150264	2789.936732	404.259081	1911.965961	407.764109	1594.143458	149.209407	50.698346	1416.144893	2577.922942
SPQLEDEAKEL	277.786221	1036.769599	654.393133	543.158332	1201.051478	532.904772	1153.984688	93.904069	227.779413	1256.263483	848.883078	11.723532	1718.711467	249.621916	232.122231	143.639516	2338.913313	3901.151115	230.170538	424.933721	1030.205023	1016.289722	9.938066	2206.949104	5638.847764	624.672814	1898.221903	1798.849490	1476.675831	906.315700	1807.089223	465.656026	2584.407912	542.809015	136.917168	1221.109312	2302.560668
SPQLEDEAKELQ	241.81852	927.04902	593.46943	412.70948	1069.11015	533.98925	801.28466	73.37816	214.17205	1128.25290	664.97569	858.80506	1447.58946	209.51772	185.81760	141.15500	1599.47307	2603.37298	284.19503	307.22308	614.62298	848.57225	844.03596	1204.66812	3106.45944	334.82910	1899.97455	1372.41877	1147.46899	452.55092	905.11587	234.48943	1240.27119	314.72025	158.90466	1060.96160	1903.28535
VGRPEWWMDYQ	1358.65238	1102.29997	889.81150	1231.63184	2599.58091	639.78954	1571.67682	247.10198	403.28590	1725.18970	2640.00610	44.69051	3200.06445	131.43542	129.04138	1423.58847	1377.74487	1899.69496	146.03149	528.95820	1174.19960	1615.34573	1051.83839	1615.29359	5583.56003	1107.01914	1930.71736	1734.28048	2425.28805	1193.97178	2159.53222	1164.79296	1945.54173	636.37644	864.14885	947.59896	1895.08407
YGGFM(+15.99)RF	308.72641	1857.00611	431.99899	1104.60674	3090.62302	1078.02620	1193.75619	144.04006	363.70816	499.25315	1458.25799	1265.20513	1295.66668	234.68305	162.85851	33.11038	2946.16832	2884.89510	343.08152	1159.78803	1007.22268	1484.29441	1485.36170	1133.40160	10249.66731	838.89131	3793.75036	4006.98441	4505.30649	534.95961	3558.76461	772.80113	2392.42032	373.12693	427.22210	1326.31802	2252.70854
YGGFM(+15.99)RGL	379.2099	2089.9072	731.6304	841.8555	2775.9645	374.2918	935.5794	83.4596	402.6122	1038.4256	1462.9972	1481.3787	1453.9900	210.7689	119.9386	1644.0987	3069.9812	3360.3432	374.7593	924.2952	817.3762	1649.4453	1548.2935	2332.4758	9752.8839	825.9417	3705.4005	4033.7214	3343.9755	635.2441	3495.1601	835.5263	3050.4199	329.4857	602.6551	2150.2488	2565.2627
YGGFMRF	497.01736	1072.45165	657.85941	390.74855	1517.08828	244.21196	1554.66620	112.81281	158.01486	1131.18459	946.43495	25.09619	2253.31242	114.42392	140.31986	66.76026	1874.88530	2053.41614	90.99779	339.80553	464.00538	570.87299	10.20850	2234.56324	5548.33404	626.14708	3144.52475	1639.39121	1949.17177	374.88962	1006.41738	379.70159	1174.01710	198.78394	20.12067	735.51331	1280.08874
YGGFMRGL	455.524465	1076.660757	731.799562	503.240530	885.183573	347.129756	1229.231896	64.953071	104.692304	976.237469	746.840484	13.584416	1732.230280	175.666854	166.674002	51.737575	1598.639631	2114.666742	142.632741	345.057006	1087.930780	1217.931336	9.304989	1577.833891	5638.117818	713.249485	2884.506078	1915.576318	1685.077620	825.545519	1258.356088	298.362835	1707.331613	515.077918	11.420737	723.209313	626.059157
EIGDEENSAKFPI(-.98)	684.13642	1410.96250	646.02682	302.45713	3245.14893	1194.65850	1627.76406	705.96206	829.37014	855.18367	660.46934	159.38188	1395.32122	824.27309	94.08887	212.89589	1681.87644	2244.52753	767.08280	420.17673	1534.93003	867.05916	72.27757	307.27640	2052.56475	814.77669	2291.23308	1853.18938	1223.98844	506.21449	744.46896	871.47618	2913.11112	347.84685	1713.70450	1711.82257	1297.38821
DDGPYRMEHFRWGSPPKD	888.0572	963.9873	778.7072	159.2630	1088.9537	3044.2984	2095.5458	682.8386	701.4690	7495.9115	412.2031	1752.1296	526.3064	357.5323	2394.6282	1438.4015	767.3897	365.3827	805.7882	745.8070	1334.7368	2395.1000	501.5079	666.1333	389.5712	1328.1925	523.2651	1088.8715	488.6027	8686.6042	227.8335	1777.8577	1591.5709	364.4288	1053.8615	1302.8425	157.8620
FKNAIIKNAH	268.18564	2262.00275	630.90863	222.67547	459.62972	538.33252	2842.81733	1521.00816	2097.98308	1872.80321	741.44975	1235.61020	431.51476	654.35859	2376.64313	2678.26587	2196.37466	19.90206	545.49302	683.86008	834.08123	1213.78134	1969.22179	1076.24002	1284.69057	2033.28923	1179.15512	2507.17002	451.98455	4786.01655	923.92415	1309.30975	1885.42008	263.12043	984.08458	1817.17792	1008.37974
FKNAIIKNAHKKGQ	1068.24973	616.22640	565.04669	360.62832	346.00555	77.54253	1326.01402	1852.36027	1833.90254	978.62750	4537.85561	261.39455	696.48980	1427.84678	943.04308	4570.06188	147.62783	671.19572	990.27794	849.31405	2653.58271	635.24536	2415.98368	1810.29062	228.90026	1771.95713	26.62369	458.20485	426.99343	1281.29942	287.09892	904.95755	90.10210	262.74748	463.27945	475.99949	47.21013
GGPEFRDDGAEPGPRE(-.98)	184.34248	409.66628	516.77914	838.62365	2540.15618	1655.25502	222.58258	519.13462	1381.73306	1554.81341	575.42936	220.52535	163.16835	447.08426	1992.40359	1841.38729	1067.70061	162.55123	1192.38880	3808.54640	3507.88639	1130.17613	72.16027	1693.86708	3408.05571	1422.56663	352.24162	255.41762	534.41627	1162.01400	350.11235	604.42017	1723.70927	184.02595	257.81121	102.00221	117.24573
GPEFRDDGAEPGPRE(-.98)	230.43919	491.78614	586.33114	1742.38708	2758.03902	1447.44269	239.64908	486.38715	1509.67262	1083.83336	1165.46144	161.95845	157.08193	404.09396	1897.64600	2055.16359	1128.97156	165.90879	1231.57062	1824.44855	4294.58862	1313.28439	92.07857	1940.39295	3481.14670	1865.25933	422.14152	306.39618	610.68631	943.73315	372.71368	598.73971	1605.97972	1744.80208	475.44030	162.96999	144.46238
KYVMGHFRWD	666.83001	919.03956	488.17867	79.26367	2276.84373	3537.79734	1259.29414	891.59384	820.76288	1853.21539	132.03477	1190.99449	216.61804	316.29118	1862.93105	847.15950	796.49801	365.55210	476.94614	1044.53757	942.44799	1692.66198	824.08453	257.70230	646.71090	908.59956	335.65493	1020.51415	171.39937	3264.04992	495.70035	1228.04311	1074.60414	287.91871	799.49838	1156.08301	545.24816
KYVMGHFRWDRF(-.98)	523.94947	610.84660	208.12384	103.28573	1553.99133	3179.39383	1145.10540	690.21057	787.75085	1489.83337	220.14246	1178.58549	222.54323	231.15933	2435.86516	1234.28548	847.97340	347.19952	568.89702	447.92820	1414.73048	1804.43796	604.92168	638.78623	195.89304	1100.33812	520.56015	443.48029	291.18103	5564.39222	135.57800	1092.37310	2722.20930	357.51755	1007.42049	1317.40521	80.29325
PEFRDDGAEPGPRE(-.98)	101.5571	596.9674	452.4494	1990.4450	2191.1090	1305.3927	318.2228	753.1191	1962.0430	1404.0559	709.4040	205.6463	160.8840	479.5994	1850.9203	1693.1350	1543.1788	225.1386	1603.9442	1974.4034	4349.6843	1117.5126	888.3964	1639.6116	2423.2787	1500.7441	666.3537	185.0070	875.8161	802.2767	332.5011	340.0470	1188.1347	1039.8707	188.8059	242.9633	173.2729
RPVKVYPNGAEDES(+79.97)AESFPLEF	11070.911012	1024.212935	598.930738	803.337809	1890.399514	5483.960323	12819.912157	1280.582473	2013.762122	2.263158	985.079174	985.226118	177.458969	149.420336	1288.865876	11322.215087	137.203384	350.236262	452.653906	1318.013793	525.399139	1313.939201	89.573796	398.426466	4241.817379	1952.205252	655.557869	1316.604545	1001.470239	4223.601885	559.535447	8715.438528	575.801552	411.634553	98.938620	314.634411	853.556459
RPVKVYPNGAEDESAESFPLEF	8413.8285	413.0344	338.3428	661.9594	3161.6411	11184.3257	3404.5756	2516.1064	1870.7808	2733.8307	998.1490	2845.4641	510.6685	106.7193	3105.8971	2646.3593	181.0622	109.3660	690.8507	1919.2375	442.4930	311.2595	120.4821	1401.7923	1986.6106	585.1426	425.6389	859.3504	318.6119	1767.5116	420.8891	7855.0619	150.8136	317.5392	130.3227	436.2797	860.9705
S(+42.01)YSMEHFRWGKPV(-.98)	1445.26051	1034.17101	594.73437	216.16841	1849.27024	5106.88113	2373.08811	762.46943	751.09516	3995.77067	222.74034	1434.68463	221.32407	273.21215	2159.03240	1318.43543	561.81899	201.60802	621.99264	1744.30736	867.82676	1931.20450	354.59992	1123.50072	1586.33718	822.79776	772.28777	1137.27354	556.57733	6273.38074	212.44451	3022.66171	2174.82932	304.06473	20.09392	1107.82212	42.29011
SQTPLVTLF	2026.3571	1338.3774	1623.4480	2445.3891	2433.8217	2375.7449	1749.4797	2302.1809	958.0414	1496.5210	1965.0195	509.4767	966.5813	992.6191	1519.5531	921.3968	731.3100	782.0178	1802.1732	1235.6303	1699.5273	241.5109	1093.2346	676.9668	3519.4247	369.1602	3336.4293	1910.7103	1857.1677	1348.9777	1192.4735	2850.4817	440.4337	347.0073	3960.2972	18.1852	1008.0168
SQTPLVTLFKNAIIKNAHKKGQ	117.48860	757.42141	280.49213	1837.08784	1090.60960	1926.86155	1054.30282	550.62580	1280.11986	26577.13347	2518.14077	162.30858	95.95411	35.02182	219.53943	1019.87965	1126.77236	786.73696	1416.79001	893.44103	2665.32701	550.16239	871.62217	4885.21030	790.21630	515.94608	1189.60516	972.49127	1543.78200	430.22349	235.00719	1618.50745	722.11728	549.73388	525.34170	826.92977	1804.46577
SYSMEHF	251.8199	454.5423	1294.8463	720.5086	1186.6389	1207.4403	477.5258	1406.0815	662.9903	1143.6044	873.6375	595.1338	544.0245	1035.8847	1347.5163	388.6288	1444.8139	1321.3567	1109.8358	1271.2487	1666.5523	596.2820	1446.0838	1652.4600	1869.7001	247.4647	752.6563	1594.6875	1185.4428	772.3699	1695.7522	1509.0425	687.0539	1371.3856	2411.2158	385.8057	1447.4501
SYSMEHFRWGKPV(-.98)	871.230465	500.403496	643.408852	162.443722	1217.779121	1200.968282	792.456632	678.602887	282.251955	4061.782860	364.162704	1137.518104	442.042424	373.295725	1345.266997	1461.102210	1093.807251	862.250912	1337.728993	685.261637	2349.972008	1047.818175	392.938806	1006.289154	482.209703	482.141417	581.026236	416.758618	566.741233	899.759385	377.526805	602.579019	621.020594	1414.679349	4.007785	846.135939	735.753967
TPLVTLFKNAIIKNAHKKGQ	39.017319	59.253908	324.591693	5997.692736	4015.516224	1727.033128	265.104454	59.435508	2515.269223	1015.082744	614.686639	1326.689093	582.734372	51.543614	2577.540941	3281.249169	145.988688	5.532145	599.201862	606.678534	2751.414666	911.412250	708.273628	2352.920690	1273.930689	3405.909709	130.065672	115.108949	123.705923	592.024646	125.156847	1279.954375	1360.806783	8028.490536	1589.838004	1710.198870	951.774009
Y(+42.01)GGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAH	14162.883902	2365.057731	158.584889	150.033360	1631.640545	9011.993295	14121.987855	459.118373	2756.309415	2474.392467	375.559132	1208.715658	1036.564495	749.624185	2058.697338	2656.479389	668.447605	511.980078	519.999158	855.164940	436.039162	3514.722470	158.205674	895.194346	3636.670696	2895.218123	2333.079053	2940.203022	744.520437	5817.330372	325.354293	13247.741149	1609.137381	196.111785	8.994823	2012.047551	640.937726
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNA	23585.955975	382.829697	561.830452	2.812048	3284.611173	19705.363557	23676.182460	387.076220	1236.833564	5527.907107	443.781787	2161.675193	54.842816	484.070825	288.411734	6380.381734	136.686925	162.916960	133.572199	430.824586	148.733429	1542.313664	560.927937	437.555832	2188.827943	2285.938157	586.843613	1073.933933	324.560096	10578.781438	137.602105	21344.819396	1093.705647	135.836551	865.835574	1553.389076	501.464470
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	10562.507025	1313.873053	326.827403	185.917882	1569.881824	6231.741689	11887.322857	875.327942	1576.701996	4496.915948	369.626719	1895.314932	116.868448	128.287745	1991.375605	3063.330306	588.820515	322.615369	504.834166	624.502360	931.560661	3005.680615	318.987323	1286.978004	3566.243306	3087.327742	2298.889006	3011.368614	702.229602	12637.042044	197.312580	8671.848646	1288.368399	153.314102	1.266135	1189.672749	92.427463
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	1665.118109	2358.463974	462.164207	323.549390	124.093425	2876.484699	1764.176098	1967.862107	737.734284	3099.549506	918.660769	536.229356	273.353854	411.823698	2090.703456	994.902695	458.077857	652.567267	1210.835641	229.356185	1213.990431	2246.736673	807.261405	565.522042	624.540004	756.459013	1449.365160	919.152149	290.393644	5464.374704	324.698935	3339.414959	716.832285	137.239539	5.673444	1017.026609	257.101993
YGGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAHKKGQ	855.61804	1564.62538	679.22428	3299.93371	988.48249	419.93398	1529.47214	1928.35277	1212.12873	2146.84750	3696.69073	189.13095	111.49999	1318.82335	375.64435	1651.57970	2915.53495	2794.01381	2534.75999	887.30389	1905.95113	297.58898	1149.79025	5203.24189	555.50651	1204.74838	6925.62624	2044.63784	3871.58467	346.47124	1266.41939	1445.10787	11.67290	590.22729	86.98747	465.23928	6528.60896
YGGFMTSE	698.4797	461.6090	926.2728	579.2999	1302.5862	1772.6989	726.7832	1327.9245	470.9490	4159.3878	559.5050	505.2308	551.4393	1257.9355	1113.2142	752.3002	1126.7745	1627.2060	1244.2337	840.4334	1524.7202	771.6526	1253.4835	1401.1738	2089.1147	255.5741	2800.7054	1989.6387	1203.5297	1502.7101	1267.6343	3296.1996	546.6067	937.7522	2665.3345	332.3717	1065.0374
YGGFMTSEKSQTPLVTLFKNAIIKNA	2951.5013	1539.9506	646.0024	689.7253	3335.0018	6548.3851	3512.8243	1398.3273	1727.1455	6010.2293	826.5009	2729.5885	184.4494	250.1372	1686.4381	7816.5240	817.2334	1608.1524	1620.6477	794.3135	2752.2311	3901.2476	426.4441	1762.2194	11793.6100	2887.3495	2554.2672	2294.5725	3100.5964	5287.8632	2175.2867	6908.9752	1365.0428	1473.6719	2038.7831	2393.6143	1054.3216
YGGFMTSEKSQTPLVTLFKNAIIKNAH	873.61538	2534.52617	1003.51082	474.94346	2619.84130	3612.68479	997.01071	1014.50509	686.67347	1824.02489	219.21242	904.18906	904.63712	304.38916	2327.82683	4316.03166	86.29545	606.95202	709.87681	444.40690	1193.59729	2882.42940	574.67644	201.99292	4608.70178	1080.22942	531.03424	2120.79391	1045.03194	2485.87129	730.94920	3774.92429	530.61881	405.83311	1057.42788	2154.77732	503.54405
YGGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	393.11266	830.16951	900.89913	1823.70062	969.88503	515.22282	1392.10677	2702.47749	2313.65046	3007.59031	3636.37601	605.44693	861.46873	863.07440	729.28256	820.22952	1335.47654	998.89814	1162.14875	437.77553	2709.20596	369.74234	1043.47270	3537.03313	310.27799	734.82812	3108.06961	817.92246	1168.32549	368.95374	819.46657	998.11605	331.29404	184.76103	60.03794	342.45879	2596.88959
ATLESVFQELGKLTGPSSQKRE	3294.04044	903.90235	935.07711	1895.27679	777.60628	2856.17627	1788.73418	959.81735	1316.80474	3300.47857	2771.12015	2015.65181	2279.14060	416.85423	2890.40177	1192.75292	1197.34697	2522.08608	5283.46813	1174.28619	1925.02997	2127.06071	1720.28421	4274.33010	1432.29168	191.30353	2295.86514	96.88988	2327.35350	216.47887	7822.12955	542.79891	430.69764	707.59705	721.83937	727.12987	1677.23823
MYEENSRDNPF	305.1265	567.2840	946.3929	379.4790	776.3466	847.9241	598.9437	973.3149	1012.5519	1420.9099	547.8667	565.5895	981.6504	751.4806	837.0393	311.9473	1301.8650	708.3824	1629.0183	609.6255	1354.0874	727.9994	1024.1684	1403.1404	2867.3674	196.5511	650.2069	1118.6491	2479.7351	434.4935	3143.0369	874.4292	525.1122	656.3637	332.9595	307.8804	417.7585
TNEIVEEQYTPQSL	2314.7539	1336.9040	3433.1293	425.7653	1255.2410	3517.1165	290.5042	1436.5918	2870.4362	3490.4357	279.9286	417.9799	1378.7863	1181.1678	2541.7544	2009.4243	703.1639	42.0380	5958.2769	3529.5288	1472.9574	1687.4461	2177.8225	3152.0782	3019.2665	656.9153	3505.1688	275.2392	4599.9721	751.0174	13376.8058	1084.1515	969.0547	677.7245	2963.3904	777.1403	136.0975
FPTLGGSQDKSLHN	664.2153	370.2542	557.7496	221.4898	597.3154	606.4768	371.3213	588.3091	372.4494	1565.7994	345.6432	698.4697	672.1565	578.0652	1128.3113	509.1754	1963.2686	864.1597	720.0531	927.4844	1430.8851	873.7425	926.7753	1476.3045	2076.4818	389.9772	2021.4806	802.8369	1225.4325	954.9039	1629.4122	434.4113	1162.6729	435.7855	1296.2335	571.3601	589.7155
TLGGSQDKSLHN	9.40251	592.52172	802.17080	561.50195	115.96206	159.53973	349.82833	1054.58435	2160.66247	1168.83266	714.69657	360.78445	885.07056	850.57742	1887.46821	1041.36511	2003.38339	294.67852	547.65671	370.16717	3213.77105	889.56429	2026.84314	2339.60508	1338.58510	596.74598	1144.12295	602.37438	1464.63799	323.35547	1665.69287	228.59093	710.10797	443.24938	434.63305	51.13244	390.57529
SVNPYLQGQRL	485.96282	411.30195	733.85188	38.58792	86.95171	817.31076	22.67851	1159.42085	513.10949	496.82094	53.22789	370.91560	607.23846	808.71197	2386.96739	196.65309	1552.83320	125.40403	1046.38220	829.46815	1821.59823	529.74321	1004.27342	1352.80673	1174.56028	277.67287	1059.35390	145.33931	1015.85492	439.73768	3538.90011	79.60038	884.72503	1232.92605	1142.59679	288.76396	30.83659
SVNPYLQGQRLDNVV	3815.52145	610.10195	851.37226	2049.88684	2490.87854	6634.58109	3752.73163	751.16707	1720.10395	2761.64171	1618.63698	1535.62826	17.36857	405.98752	774.78039	3009.91874	429.25437	506.77740	1262.37252	1164.57054	2597.84915	685.81527	242.01545	2403.89090	4948.88733	2261.88994	2771.05251	1594.16713	2287.64083	4374.91678	991.23702	5924.71792	728.08695	1855.16075	1542.86184	609.48502	624.73813
SVNPYLQGQRLDNVVA	2694.0518	647.5007	673.2173	1477.8779	2094.4568	3090.5216	2525.7932	720.1189	1055.1988	3077.7936	1142.0299	1543.8883	530.1360	405.8454	1761.6106	1651.9937	1074.6270	621.1074	1130.0799	913.4880	3208.9678	978.3610	404.5577	3778.7130	3976.7559	1346.4645	2928.0116	1292.0485	2099.3698	3167.2281	1268.3325	3335.1360	1377.1888	1314.7793	1541.2214	341.3430	602.0742
SANSNPAM(+15.99)APRE	1260.112708	2407.584605	1322.967798	1138.071781	781.401032	21.081017	916.543676	30.822463	568.511184	688.646946	1801.814999	1498.654531	958.876436	45.279093	5.431026	35.691451	4102.192382	2906.255234	270.550403	162.012907	1802.270129	1201.215803	1611.176928	4154.590623	3845.167459	946.164790	1575.399704	2388.857335	6502.607984	125.496761	3124.517422	31.557790	2130.711937	297.813342	1347.675117	2533.847678	1858.003876
SANSNPAMAPRE	216.84933	1064.92141	1023.03393	632.29622	633.01556	56.89700	1342.72703	64.95270	324.50022	1817.11808	731.77210	32.48293	844.89077	48.98649	187.64042	84.60936	3282.09110	1949.56949	99.86112	430.44818	1768.89111	620.53899	15.36907	3199.86188	3633.86203	1038.03566	2087.23858	3026.89867	2434.76128	309.08295	1282.94845	86.84305	1642.58491	474.95798	126.71698	834.54089	1060.56441

Log2 transformation

Data transformation applies a mathematical transformation on individual values themselves. For mass spec data, log transformation is a good choice, as it reduces or removes the skewness of mass spec data.

Code

plot_grid(hist_log2, qq_log2, pca_log2, nrow = 1)

Code

#rownames(log2_d1) == feature_name$variable
rownames(log2_d1) = feature_name$name
# display table
log2_d1 %>% 
        mutate(across(everything(), round, digit=2)) %>%        
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

	Pituitary_53	Pituitary_31	Pituitary_38	Pituitary_63	Pituitary_55	Pituitary_51	Pituitary_50	Pituitary_34	Pituitary_59	Pituitary_43	Pituitary_66	Pituitary_26	Pituitary_19	Pituitary_24	Pituitary_41	Pituitary_57	Pituitary_47	Pituitary_52	Pituitary_23	Pituitary_58	Pituitary_44	Pituitary_37	Pituitary_39	Pituitary_46	Pituitary_65	Pituitary_56	Pituitary_48	Pituitary_35	Pituitary_61	Pituitary_49	Pituitary_60	Pituitary_54	Pituitary_45	Pituitary_42	Pituitary_62	Pituitary_25	Pituitary_64
AGAPEPAEPMELAKPSA	13.04	9.60	9.80	3.51	10.60	14.04	12.86	4.61	10.12	12.22	8.90	10.40	2.15	9.61	12.55	13.85	10.01	10.66	9.91	4.75	11.99	10.36	10.05	10.11	6.77	8.89	10.17	10.16	9.90	12.55	9.51	12.70	5.33	5.51	7.06	10.73	9.94
LAGAPEPA	10.68	9.17	9.93	5.52	9.27	12.58	12.48	6.63	5.61	10.49	6.97	13.12	7.35	7.83	9.77	13.06	7.03	10.04	3.93	6.11	1.57	12.27	5.06	5.34	6.02	11.11	6.37	10.99	7.65	12.47	5.79	12.27	6.51	6.20	7.99	12.55	7.77
AFGPRGPGLQL	9.10	9.34	9.56	8.43	10.25	9.63	9.78	9.67	4.38	11.44	8.48	8.84	9.65	9.43	9.65	9.10	9.21	8.38	8.89	9.29	10.21	9.14	8.50	11.24	12.05	8.90	10.61	10.19	11.23	9.99	11.49	11.06	10.03	8.83	9.22	7.49	9.69
AAMDLEL	9.04	3.70	9.77	10.25	12.86	4.67	8.22	9.85	9.43	8.55	9.30	6.96	9.62	9.90	11.14	9.39	8.81	8.24	10.53	9.70	9.26	9.40	9.52	9.98	4.51	9.90	8.70	5.84	8.79	9.11	12.00	10.53	8.91	9.67	10.12	6.86	7.11
AELDQLLHY	10.57	9.97	8.32	10.90	11.54	11.13	6.18	10.89	11.29	12.06	11.71	9.75	11.40	7.30	9.64	12.33	9.38	8.37	12.13	10.14	11.30	11.07	7.87	11.73	10.48	8.49	9.54	7.93	7.73	10.32	9.47	9.89	11.02	10.63	9.26	9.64	9.49
EDREEASLQDRQYASHHT	5.40	9.64	10.27	9.33	7.52	9.10	8.94	10.25	10.18	11.01	10.07	10.06	8.58	9.94	7.95	9.20	10.65	9.38	10.60	7.43	11.42	8.01	10.00	11.48	9.45	9.47	8.51	10.46	10.46	8.59	9.58	7.08	9.46	9.47	9.31	8.80	9.02
EDREEASLQDRQYASHHTTE	6.69	9.04	9.82	9.05	7.74	9.07	8.96	9.93	9.64	10.92	9.05	9.58	8.69	10.06	9.13	9.33	10.65	9.39	10.56	7.88	11.53	7.98	10.27	12.10	9.41	9.38	9.37	10.18	10.46	8.96	10.45	8.26	9.68	7.70	1.56	9.06	10.02
EEASLQDRQYASHHT	5.81	9.17	10.37	9.71	5.79	8.66	8.63	10.62	10.60	10.83	10.31	10.06	8.70	9.88	7.52	7.80	10.29	9.02	10.52	7.98	11.16	7.96	10.32	11.43	10.04	7.71	8.67	10.59	10.74	6.67	9.95	6.16	8.79	6.79	2.11	8.98	9.50
EEASLQDRQYASHHTTE	7.13	8.95	10.07	9.16	7.77	9.04	9.10	10.36	9.88	10.76	9.35	9.62	8.91	9.95	8.77	9.28	10.81	9.30	10.43	8.06	11.22	8.28	10.21	11.87	10.05	9.18	9.43	10.39	11.00	8.53	10.64	8.42	9.15	7.09	4.66	8.97	10.25
EESEESEEGTTSEVT	7.99	8.63	10.51	9.03	8.84	7.81	8.80	11.25	9.65	8.53	10.46	8.63	10.59	12.98	6.89	8.66	11.55	8.69	11.07	10.81	11.23	8.34	10.35	11.15	11.09	7.21	8.15	11.52	11.19	9.03	11.01	8.73	8.51	6.04	11.03	9.57	9.95
ELDQLLHY	10.01	10.56	10.06	9.39	9.94	9.30	9.41	9.99	10.34	10.81	10.45	8.85	11.07	9.65	10.41	9.74	10.52	8.32	10.39	9.62	10.82	9.11	9.63	11.81	11.41	8.24	11.27	10.47	10.93	6.61	9.95	8.71	9.21	5.04	9.84	7.61	10.22
FLGEAYHHVPE	8.95	8.33	9.36	8.53	9.52	9.30	8.32	9.40	6.85	11.18	8.55	8.78	9.89	8.80	10.29	10.55	8.23	7.03	10.90	10.01	9.39	10.97	7.99	10.79	10.59	7.00	8.88	8.19	8.96	9.26	8.82	7.35	10.24	10.31	4.55	10.06	8.35
FLGEAYHHVPES	8.91	9.35	10.03	8.37	9.72	9.01	9.42	10.37	7.82	11.13	9.49	9.44	10.33	8.98	9.04	9.05	9.72	10.10	10.56	10.16	9.90	10.17	8.02	10.47	10.68	6.18	9.30	9.33	11.01	8.78	9.62	7.69	9.90	7.01	7.74	9.01	8.16
FLGEAYHHVPESQ	8.74	9.57	9.83	8.67	9.72	6.30	9.61	10.45	7.96	11.18	8.86	9.66	9.66	9.55	8.86	9.12	9.80	8.23	10.34	9.84	9.72	9.21	7.53	11.45	10.74	7.27	10.05	10.22	11.01	6.40	9.65	8.95	9.96	8.52	8.06	9.14	8.98
FLGEAYHHVPESQRD	7.95	8.93	9.56	8.91	9.40	8.54	8.80	9.79	7.80	11.19	8.35	8.43	9.45	9.61	10.00	9.04	10.82	8.81	10.47	9.73	10.68	9.23	8.50	12.49	10.12	7.72	11.25	9.91	10.47	9.14	10.63	9.40	10.28	9.43	4.33	8.79	9.05
FLGEAYHHVPESQRDKA	6.00	8.73	9.47	9.43	8.43	8.68	8.72	9.70	7.86	11.23	7.50	9.10	8.88	9.68	9.91	9.54	10.82	8.03	10.40	9.41	10.15	10.59	9.39	12.41	9.33	7.66	10.61	9.25	10.39	9.19	11.12	9.26	11.17	8.25	9.89	9.56	9.57
GEAYHHVPESQRD	6.76	9.37	10.73	8.46	7.57	6.74	8.88	10.24	8.80	10.99	9.83	9.61	10.53	10.08	10.63	10.72	9.83	7.33	10.63	8.74	10.73	10.15	10.53	11.71	9.95	8.30	9.80	10.26	10.65	8.42	11.49	9.05	9.03	8.37	9.54	9.77	9.65
GEAYHHVPESQRDKA	3.58	8.63	9.67	8.97	7.91	8.64	7.98	9.52	8.59	10.91	7.45	9.98	9.95	9.42	10.87	10.28	10.27	6.85	10.11	8.74	9.96	11.21	11.01	12.15	9.49	6.91	9.65	8.28	10.28	8.76	11.67	8.35	10.53	7.98	9.85	8.84	9.15
GVLFNPYYDPLQWKSSRFE	12.69	9.77	9.42	8.88	9.76	10.07	11.92	8.37	9.91	12.94	9.09	11.36	9.97	7.77	10.52	12.66	10.16	7.67	10.04	8.62	10.71	11.11	9.91	12.09	9.94	10.71	11.27	9.78	12.23	10.36	10.74	13.55	8.88	11.09	10.23	10.17	10.93
LDQLLHY	8.11	9.63	9.81	8.82	9.97	8.13	8.17	10.96	9.87	11.65	9.09	7.78	11.28	9.55	10.30	9.28	10.04	9.06	10.78	10.15	11.08	10.50	9.76	11.59	10.47	7.35	10.54	9.50	9.73	8.03	10.13	8.60	10.51	10.06	10.35	8.83	9.55
LGEAYHHVPESQRD	7.39	9.11	9.57	8.70	9.38	5.44	7.59	9.89	6.99	11.56	7.39	7.57	9.72	9.78	9.90	9.49	10.92	8.01	10.76	9.78	10.86	9.69	7.52	12.50	10.32	6.43	11.19	9.51	10.17	8.44	10.84	9.68	11.09	9.02	9.53	8.93	5.32
LGVLFNPYYDPLQWKSSRFE	13.08	9.29	9.36	11.03	12.12	11.17	13.40	10.08	10.92	13.16	10.70	11.32	8.71	8.29	8.79	13.64	9.51	9.66	10.39	9.71	11.61	11.14	7.47	13.50	11.01	12.16	12.03	11.03	12.36	12.94	12.45	14.02	10.87	10.84	10.76	8.99	10.70
Q(-17.03)KIAEKFSQ	8.62	9.95	10.61	7.45	6.26	9.30	3.43	10.98	8.38	9.63	7.91	7.88	8.63	11.19	9.76	7.92	9.63	9.18	10.19	10.02	9.91	8.69	10.01	10.95	10.43	8.43	10.49	8.22	11.09	8.52	11.41	6.21	9.59	6.97	9.80	8.29	6.63
Q(-17.03)KIAEKFSQR(-.98)	3.76	8.69	9.74	5.99	5.28	9.05	2.44	10.25	8.52	9.46	6.28	8.30	8.71	10.31	10.47	8.80	10.86	7.85	10.48	10.41	11.22	9.56	10.70	11.74	10.07	9.46	10.24	7.66	9.81	9.51	11.89	6.92	10.81	8.67	8.28	9.29	6.69
Q(-17.03)YDRVAELDQLLHY	14.00	7.78	8.34	11.67	11.81	11.64	13.72	9.74	11.37	12.97	11.03	10.50	8.60	8.08	9.81	13.92	9.73	8.28	9.71	9.83	11.21	11.01	5.53	11.98	12.27	11.86	11.59	9.40	11.67	12.34	12.00	15.05	11.60	12.15	6.58	9.37	9.15
QYDRVAELDQLLHY	10.80	6.79	10.95	11.59	12.13	10.57	11.50	10.76	11.10	11.90	11.59	9.10	9.46	8.98	10.23	11.09	8.57	8.54	10.45	9.24	11.99	10.55	8.58	2.30	11.01	10.22	9.18	10.10	10.13	10.46	10.51	12.72	11.03	10.55	5.91	8.73	10.20
RVLTEEEEKELENL	10.55	10.54	10.86	8.73	10.30	12.08	10.78	11.73	10.61	10.73	9.79	9.11	9.65	11.64	11.26	10.23	8.50	8.09	12.37	12.15	10.78	10.03	10.52	10.19	10.77	10.13	10.55	10.24	11.76	11.18	13.38	8.67	10.02	9.42	6.98	9.37	7.82
SQGGEPGAYLTPDT	9.87	9.98	9.82	8.47	9.92	8.24	8.88	9.77	9.16	10.20	8.32	9.74	9.78	9.33	9.91	8.62	10.37	9.44	10.46	8.88	9.87	9.44	8.97	11.78	10.91	7.16	8.61	9.60	10.07	8.68	9.97	9.60	9.29	8.23	9.15	9.02	10.00
SQGGEPGAYLTPDTREE	8.84	8.77	9.30	8.37	10.16	8.85	8.97	8.95	9.18	10.37	8.61	9.14	9.81	9.75	9.28	9.27	10.26	9.40	10.34	10.01	9.59	8.93	8.98	10.82	9.64	7.51	10.34	8.78	9.51	9.02	9.83	9.21	9.43	8.32	9.81	8.59	9.60
SSQEGNPPSEERGHTLQEPEEAKVGE	8.08	9.51	9.27	8.77	10.08	9.93	10.30	9.97	9.15	10.89	8.94	10.10	9.32	10.25	9.43	10.84	10.84	9.58	11.02	9.19	10.99	9.74	9.19	11.86	11.36	9.62	10.87	10.74	9.97	10.69	9.88	10.30	11.00	7.58	7.55	10.72	9.86
VAELDQLLHY	9.47	10.70	9.96	10.98	11.73	10.72	10.09	10.61	10.87	7.10	10.78	8.98	10.38	9.10	10.57	10.96	9.08	8.96	11.06	9.95	11.40	10.39	8.52	12.45	10.73	9.33	9.99	10.26	10.19	10.18	10.54	11.37	10.31	10.15	10.19	7.82	9.08
YDRVAELDQLLHY	10.91	9.61	10.21	12.18	12.35	11.10	10.65	10.19	11.75	11.86	12.03	9.26	9.16	7.41	11.03	13.06	7.60	6.96	10.97	10.45	12.01	11.56	6.87	10.03	11.70	10.36	8.67	6.97	9.07	11.61	10.73	12.92	11.67	12.06	10.38	9.76	9.53
Q(-17.03)EPGAPAAGM	10.21	9.17	9.60	9.26	10.22	11.08	10.46	9.66	9.07	10.48	9.11	9.58	9.42	9.43	9.76	9.99	10.58	10.27	10.19	9.77	10.45	9.58	9.25	10.69	11.43	8.76	7.22	11.00	10.98	11.02	11.05	10.82	9.97	9.47	10.94	9.34	10.02
SLDSPAGPA	10.46	9.22	9.81	9.23	9.78	9.97	10.25	6.53	10.22	9.54	9.14	9.67	9.34	7.39	5.97	10.12	12.28	11.44	5.91	7.76	10.38	9.51	10.34	11.85	12.58	9.43	12.58	12.31	10.51	8.82	11.33	8.79	10.94	5.82	9.90	11.27	11.68
SLDSPAGPAE	7.81	9.60	10.15	8.34	9.62	7.84	10.05	6.79	10.59	8.53	8.76	9.85	8.61	8.42	5.29	2.66	12.52	11.46	2.70	7.01	9.61	9.50	10.16	11.95	12.17	7.40	12.57	11.41	10.32	7.61	10.69	7.36	11.00	7.88	2.53	10.89	11.48
VKVGVNGF	11.11	9.78	8.29	10.44	11.97	11.08	8.47	8.27	11.55	9.52	9.50	10.52	9.08	8.87	11.31	9.51	10.54	6.92	9.81	9.80	10.47	10.96	9.62	11.05	13.05	10.28	10.34	7.73	8.30	9.56	8.20	10.27	11.39	12.18	10.54	10.49	9.89
Q(-17.03)HWSYGLRPG(-.98)	9.68	9.79	9.09	9.16	9.81	7.29	10.37	8.39	8.09	10.27	9.55	5.79	9.61	8.45	7.05	6.48	11.09	11.09	6.02	8.35	10.03	8.09	2.83	10.39	10.39	9.13	11.04	10.53	11.09	9.25	10.08	7.45	10.60	9.96	5.07	9.09	9.05
SVSTVLTSKYR	9.00	10.06	9.30	9.30	11.68	11.45	7.60	8.97	10.28	9.72	9.54	10.05	7.94	9.78	9.18	8.36	10.85	6.36	10.02	11.36	9.67	10.81	9.48	10.55	11.42	8.59	9.74	6.21	7.21	10.19	9.22	9.70	10.94	10.62	10.82	10.59	10.26
GVANALSHKYH	6.41	10.47	9.48	10.23	10.81	8.89	7.85	9.75	11.08	10.61	10.23	9.68	7.77	10.29	9.71	10.06	12.04	6.38	10.75	10.81	10.80	11.17	6.17	11.14	11.13	10.59	5.94	8.90	6.86	10.34	7.31	9.83	11.46	11.10	5.93	4.28	10.19
KVVAGVANALSHKYH	10.34	10.26	9.02	9.74	11.21	10.01	7.79	8.90	10.20	10.91	9.64	9.85	10.47	10.21	10.15	10.07	11.98	10.53	11.00	10.49	11.00	11.40	10.27	11.38	11.04	10.21	10.37	8.56	10.73	11.12	10.74	10.21	11.75	11.47	10.55	10.36	9.92
VANALSHKYH	6.08	10.56	9.69	11.12	9.82	8.45	8.45	9.79	12.10	10.11	11.06	9.43	8.16	10.30	9.72	10.79	11.18	5.63	9.81	9.66	10.70	11.65	5.84	10.92	10.86	10.97	10.64	8.31	5.75	10.62	7.59	10.15	10.16	10.75	6.02	9.87	10.57
GRTLYGFGG	7.72	10.03	8.19	10.28	11.08	11.00	7.94	9.31	10.79	7.40	10.12	6.87	9.52	9.61	10.77	8.63	11.23	8.45	10.30	10.47	10.55	10.77	6.99	10.62	12.60	8.83	8.03	9.25	9.20	9.72	8.64	9.90	11.65	10.71	10.56	6.59	5.81
RTLYGFGG	7.80	9.93	7.78	10.58	11.30	10.73	7.45	9.12	11.08	8.23	10.10	6.90	9.33	9.63	10.58	8.37	11.33	8.33	10.09	10.38	10.37	10.82	7.58	10.22	12.81	9.10	8.15	9.26	9.29	9.17	9.14	9.54	11.64	11.30	10.65	7.22	6.82
TLYGFGG	10.07	11.36	10.37	11.13	12.06	11.40	11.90	7.84	11.40	8.76	11.17	5.19	12.44	7.78	10.92	9.69	9.82	11.91	8.81	8.67	8.98	10.58	10.18	9.77	12.36	8.99	12.00	10.95	11.12	8.32	9.95	8.97	10.64	11.96	8.55	9.14	10.36
AADQDLGPEAPPEGVLGA	11.50	9.39	7.47	8.49	10.36	10.30	12.25	10.04	9.58	11.67	9.56	10.50	8.95	6.86	10.59	10.69	9.59	7.45	8.84	8.94	9.67	10.37	9.02	9.84	10.32	10.06	10.97	10.60	9.72	11.06	8.81	11.64	10.15	7.85	10.08	10.85	11.12
AADQDLGPEAPPEGVLGAL	14.30	9.90	7.68	12.64	13.06	11.91	14.44	11.53	11.57	13.92	11.22	11.23	7.36	9.12	10.97	13.23	9.69	9.94	9.96	8.18	11.94	10.77	10.00	12.35	12.98	12.59	11.57	10.20	11.11	13.13	9.88	15.14	11.73	13.31	9.79	11.25	11.39
LENPQPQAPARRLLPP	10.22	9.72	8.78	8.94	9.86	9.65	10.44	7.56	7.11	9.93	9.53	9.93	9.84	8.72	9.69	9.61	9.71	10.62	8.04	8.89	9.61	9.68	7.69	10.32	11.64	9.69	10.06	10.17	10.48	11.18	10.08	9.61	10.96	8.95	5.10	10.35	9.29
VKMALQQEGFD	10.49	9.69	8.67	7.90	11.20	12.48	11.37	9.30	10.15	9.61	8.01	10.75	9.28	8.39	10.34	10.04	10.20	10.34	8.98	9.49	9.51	10.00	8.60	8.63	11.84	9.97	9.72	10.92	10.10	12.13	9.18	10.84	10.37	8.53	8.59	9.78	7.77
GGFMRGL	10.55	10.72	9.21	10.55	8.95	7.47	9.08	10.02	9.87	9.58	10.08	10.63	12.31	6.50	7.06	7.98	9.71	11.26	9.36	8.87	9.63	11.76	6.15	10.60	12.05	9.20	10.11	10.97	6.84	9.34	9.39	9.79	12.15	11.00	10.93	10.31	9.71
Q(-17.03)LEDEAKELQ	9.60	10.53	9.47	8.84	10.69	9.68	7.34	7.21	8.26	10.35	9.83	10.30	10.94	7.73	10.73	7.72	11.01	12.00	7.47	8.69	10.62	10.37	10.22	10.32	12.36	9.58	11.18	11.54	10.53	10.06	10.42	9.51	10.80	9.18	6.52	10.74	12.24
SPQLEDE	8.11	10.45	9.76	10.66	9.08	7.30	10.43	7.44	9.07	9.23	11.06	1.91	10.97	7.52	10.67	7.24	11.27	11.56	7.40	8.43	9.93	10.64	10.19	11.01	12.86	10.52	11.54	12.31	11.45	8.66	10.90	8.67	10.64	7.22	5.66	10.47	11.33
SPQLEDEAKEL	8.12	10.02	9.35	9.09	10.23	9.06	10.17	6.55	7.83	10.29	9.73	3.55	10.75	7.96	7.86	7.17	11.19	11.93	7.85	8.73	10.01	9.99	3.31	11.11	12.46	9.29	10.89	10.81	10.53	9.82	10.82	8.86	11.34	9.08	7.10	10.25	11.17
SPQLEDEAKELQ	7.92	9.86	9.21	8.69	10.06	9.06	9.65	6.20	7.74	10.14	9.38	9.75	10.50	7.71	7.54	7.14	10.64	11.35	8.15	8.26	9.26	9.73	9.72	10.23	11.60	8.39	10.89	10.42	10.16	8.82	9.82	7.87	10.28	8.30	7.31	10.05	10.89
VGRPEWWMDYQ	10.41	10.11	9.80	10.27	11.34	9.32	10.62	7.95	8.66	10.75	11.37	5.48	11.64	7.04	7.01	10.48	10.43	10.89	7.19	9.05	10.20	10.66	10.04	10.66	12.45	10.11	10.91	10.76	11.24	10.22	11.08	10.19	10.93	9.31	9.76	9.89	10.89
YGGFM(+15.99)RF	8.27	10.86	8.75	10.11	11.59	10.07	10.22	7.17	8.51	8.96	10.51	10.31	10.34	7.87	7.35	5.05	11.52	11.49	8.42	10.18	9.98	10.54	10.54	10.15	13.32	9.71	11.89	11.97	12.14	9.06	11.80	9.59	11.22	8.54	8.74	10.37	11.14
YGGFM(+15.99)RGL	8.57	11.03	9.51	9.72	11.44	8.55	9.87	6.38	8.65	10.02	10.51	10.53	10.51	7.72	6.91	10.68	11.58	11.71	8.55	9.85	9.67	10.69	10.60	11.19	13.25	9.69	11.86	11.98	11.71	9.31	11.77	9.71	11.57	8.36	9.24	11.07	11.32
YGGFMRF	8.96	10.07	9.36	8.61	10.57	7.93	10.60	6.82	7.30	10.14	9.89	4.65	11.14	6.84	7.13	6.06	10.87	11.00	6.51	8.41	8.86	9.16	3.35	11.13	12.44	9.29	11.62	10.68	10.93	8.55	9.98	8.57	10.20	7.64	4.33	9.52	10.32
YGGFMRGL	8.83	10.07	9.52	8.98	9.79	8.44	10.26	6.02	6.71	9.93	9.54	3.76	10.76	7.46	7.38	5.69	10.64	11.05	7.16	8.43	10.09	10.25	3.22	10.62	12.46	9.48	11.49	10.90	10.72	9.69	10.30	8.22	10.74	9.01	3.51	9.50	9.29
EIGDEENSAKFPI(-.98)	9.42	10.46	9.34	8.24	11.66	10.22	10.67	9.46	9.70	9.74	9.37	7.32	10.45	9.69	6.56	7.73	10.72	11.13	9.58	8.71	10.58	9.76	6.18	8.26	11.00	9.67	11.16	10.86	10.26	8.98	9.54	9.77	11.51	8.44	10.74	10.74	10.34
DDGPYRMEHFRWGSPPKD	9.79	9.91	9.60	7.32	10.09	11.57	11.03	9.42	9.45	12.87	8.69	10.77	9.04	8.48	11.23	10.49	9.58	8.51	9.65	9.54	10.38	11.23	8.97	9.38	8.61	10.38	9.03	10.09	8.93	13.08	7.83	10.80	10.64	8.51	10.04	10.35	7.30
FKNAIIKNAH	8.07	11.14	9.30	7.80	8.84	9.07	11.47	10.57	11.03	10.87	9.53	10.27	8.75	9.35	11.21	11.39	11.10	4.31	9.09	9.42	9.70	10.25	10.94	10.07	10.33	10.99	10.20	11.29	8.82	12.22	9.85	10.35	10.88	8.04	9.94	10.83	9.98
FKNAIIKNAHKKGQ	10.06	9.27	9.14	8.49	8.43	6.28	10.37	10.86	10.84	9.93	12.15	8.03	9.44	10.48	9.88	12.16	7.21	9.39	9.95	9.73	11.37	9.31	11.24	10.82	7.84	10.79	4.73	8.84	8.74	10.32	8.17	9.82	6.49	8.04	8.86	8.89	5.56
GGPEFRDDGAEPGPRE(-.98)	7.53	8.68	9.01	9.71	11.31	10.69	7.80	9.02	10.43	10.60	9.17	7.78	7.35	8.80	10.96	10.85	10.06	7.34	10.22	11.90	11.78	10.14	6.17	10.73	11.73	10.47	8.46	8.00	9.06	10.18	8.45	9.24	10.75	7.52	8.01	6.67	6.87
GPEFRDDGAEPGPRE(-.98)	7.85	8.94	9.20	10.77	11.43	10.50	7.90	8.93	10.56	10.08	10.19	7.34	7.30	8.66	10.89	11.01	10.14	7.37	10.27	10.83	12.07	10.36	6.52	10.92	11.77	10.87	8.72	8.26	9.25	9.88	8.54	9.23	10.65	10.77	8.89	7.35	7.17
KYVMGHFRWD	9.38	9.84	8.93	6.31	11.15	11.79	10.30	9.80	9.68	10.86	7.04	10.22	7.76	8.31	10.86	9.73	9.64	8.51	8.90	10.03	9.88	10.73	9.69	8.01	9.34	9.83	8.39	10.00	7.42	11.67	8.95	10.26	10.07	8.17	9.64	10.18	9.09
KYVMGHFRWDRF(-.98)	9.03	9.25	7.70	6.69	10.60	11.63	10.16	9.43	9.62	10.54	7.78	10.20	7.80	7.85	11.25	10.27	9.73	8.44	9.15	8.81	10.47	10.82	9.24	9.32	7.61	10.10	9.02	8.79	8.19	12.44	7.08	10.09	11.41	8.48	9.98	10.36	6.33
PEFRDDGAEPGPRE(-.98)	6.67	9.22	8.82	10.96	11.10	10.35	8.31	9.56	10.94	10.46	9.47	7.68	7.33	8.91	10.85	10.73	10.59	7.81	10.65	10.95	12.09	10.13	9.80	10.68	11.24	10.55	9.38	7.53	9.77	9.65	8.38	8.41	10.21	10.02	7.56	7.92	7.44
RPVKVYPNGAEDES(+79.97)AESFPLEF	13.43	10.00	9.23	9.65	10.88	12.42	13.65	10.32	10.98	1.18	9.94	9.94	7.47	7.22	10.33	13.47	7.10	8.45	8.82	10.36	9.04	10.36	6.49	8.64	12.05	10.93	9.36	10.36	9.97	12.04	9.13	13.09	9.17	8.69	6.63	8.30	9.74
RPVKVYPNGAEDESAESFPLEF	13.04	8.69	8.40	9.37	11.63	13.45	11.73	11.30	10.87	11.42	9.96	11.47	9.00	6.74	11.60	11.37	7.50	6.77	9.43	10.91	8.79	8.28	6.91	10.45	10.96	9.19	8.73	9.75	8.32	10.79	8.72	12.94	7.24	8.31	7.03	8.77	9.75
S(+42.01)YSMEHFRWGKPV(-.98)	10.50	10.01	9.22	7.76	10.85	12.32	11.21	9.57	9.55	11.96	7.80	10.49	7.79	8.09	11.08	10.36	9.13	7.66	9.28	10.77	9.76	10.92	8.47	10.13	10.63	9.68	9.59	10.15	9.12	12.62	7.73	11.56	11.09	8.25	4.33	10.11	5.40
SQTPLVTLF	10.98	10.39	10.66	11.26	11.25	11.21	10.77	11.17	9.90	10.55	10.94	8.99	9.92	9.96	10.57	9.85	9.51	9.61	10.82	10.27	10.73	7.92	10.09	9.40	11.78	8.53	11.70	10.90	10.86	10.40	10.22	11.48	8.78	8.44	11.95	4.18	9.98
SQTPLVTLFKNAIIKNAHKKGQ	6.88	9.56	8.13	10.84	10.09	10.91	10.04	9.10	10.32	14.70	11.30	7.34	6.58	5.13	7.78	9.99	10.14	9.62	10.47	9.80	11.38	9.10	9.77	12.25	9.63	9.01	10.22	9.93	10.59	8.75	7.88	10.66	9.50	9.10	9.04	9.69	10.82
SYSMEHF	7.98	8.83	10.34	9.49	10.21	10.24	8.90	10.46	9.37	10.16	9.77	9.22	9.09	10.02	10.40	8.60	10.50	10.37	10.12	10.31	10.70	9.22	10.50	10.69	10.87	7.95	9.56	10.64	10.21	9.59	10.73	10.56	9.42	10.42	11.24	8.59	10.50
SYSMEHFRWGKPV(-.98)	9.77	8.97	9.33	7.34	10.25	10.23	9.63	9.41	8.14	11.99	8.51	10.15	8.79	8.54	10.39	10.51	10.10	9.75	10.39	9.42	11.20	10.03	8.62	9.97	8.91	8.91	9.18	8.70	9.15	9.81	8.56	9.24	9.28	10.47	2.00	9.72	9.52
TPLVTLFKNAIIKNAHKKGQ	5.29	5.89	8.34	12.55	11.97	10.75	8.05	5.89	11.30	9.99	9.26	10.37	9.19	5.69	11.33	11.68	7.19	2.47	9.23	9.24	11.43	9.83	9.47	11.20	10.32	11.73	7.02	6.85	6.95	9.21	6.97	10.32	10.41	12.97	10.63	10.74	9.89
Y(+42.01)GGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAH	13.79	11.21	7.31	7.23	10.67	13.14	13.79	8.84	11.43	11.27	8.55	10.24	10.02	9.55	11.01	11.38	9.38	9.00	9.02	9.74	8.77	11.78	7.31	9.81	11.83	11.50	11.19	11.52	9.54	12.51	8.35	13.69	10.65	7.62	3.17	10.97	9.32
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNA	14.53	8.58	9.13	1.49	11.68	14.27	14.53	8.60	10.27	12.43	8.79	11.08	5.78	8.92	8.17	12.64	7.09	7.35	7.06	8.75	7.22	10.59	9.13	8.77	11.10	11.16	9.20	10.07	8.34	13.37	7.10	14.38	10.10	7.09	9.76	10.60	8.97
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	13.37	10.36	8.35	7.54	10.62	12.61	13.54	9.77	10.62	12.13	8.53	10.89	6.87	7.00	10.96	11.58	9.20	8.33	8.98	9.29	9.86	11.55	8.32	10.33	11.80	11.59	11.17	11.56	9.46	13.63	7.62	13.08	10.33	7.26	0.34	10.22	6.53
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	10.70	11.20	8.85	8.34	6.96	11.49	10.78	10.94	9.53	11.60	9.84	9.07	8.09	8.69	11.03	9.96	8.84	9.35	10.24	7.84	10.25	11.13	9.66	9.14	9.29	9.56	10.50	9.84	8.18	12.42	8.34	11.71	9.49	7.10	2.50	9.99	8.01
YGGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAHKKGQ	9.74	10.61	9.41	11.69	9.95	8.71	10.58	10.91	10.24	11.07	11.85	7.56	6.80	10.37	8.55	10.69	11.51	11.45	11.31	9.79	10.90	8.22	10.17	12.35	9.12	10.23	12.76	11.00	11.92	8.44	10.31	10.50	3.55	9.21	6.44	8.86	12.67
YGGFMTSE	9.45	8.85	9.86	9.18	10.35	10.79	9.51	10.37	8.88	12.02	9.13	8.98	9.11	10.30	10.12	9.56	10.14	10.67	10.28	9.71	10.57	9.59	10.29	10.45	11.03	8.00	11.45	10.96	10.23	10.55	10.31	11.69	9.09	9.87	11.38	8.38	10.06
YGGFMTSEKSQTPLVTLFKNAIIKNA	11.53	10.59	9.34	9.43	11.70	12.68	11.78	10.45	10.75	12.55	9.69	11.41	7.53	7.97	10.72	12.93	9.67	10.65	10.66	9.63	11.43	11.93	8.74	10.78	13.53	11.50	11.32	11.16	11.60	12.37	11.09	12.75	10.41	10.53	10.99	11.22	10.04
YGGFMTSEKSQTPLVTLFKNAIIKNAH	9.77	11.31	9.97	8.89	11.36	11.82	9.96	9.99	9.42	10.83	7.78	9.82	9.82	8.25	11.18	12.08	6.43	9.25	9.47	8.80	10.22	11.49	9.17	7.66	12.17	10.08	9.05	11.05	10.03	11.28	9.51	11.88	9.05	8.66	10.05	11.07	8.98
YGGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	8.62	9.70	9.82	10.83	9.92	9.01	10.44	11.40	11.18	11.55	11.83	9.24	9.75	9.75	9.51	9.68	10.38	9.96	10.18	8.77	11.40	8.53	10.03	11.79	8.28	9.52	11.60	9.68	10.19	8.53	9.68	9.96	8.37	7.53	5.91	8.42	11.34
ATLESVFQELGKLTGPSSQKRE	11.69	9.82	9.87	10.89	9.60	11.48	10.80	9.91	10.36	11.69	11.44	10.98	11.15	8.70	11.50	10.22	10.23	11.30	12.37	10.20	10.91	11.05	10.75	12.06	10.48	7.58	11.16	6.60	11.18	7.76	12.93	9.08	8.75	9.47	9.50	9.51	10.71
MYEENSRDNPF	8.25	9.15	9.89	8.57	9.60	9.73	9.23	9.93	9.98	10.47	9.10	9.14	9.94	9.55	9.71	8.29	10.35	9.47	10.67	9.25	10.40	9.51	10.00	10.45	11.49	7.62	9.34	10.13	11.28	8.76	11.62	9.77	9.04	9.36	8.38	8.27	8.71
TNEIVEEQYTPQSL	11.18	10.38	11.75	8.73	10.29	11.78	8.18	10.49	11.49	11.77	8.13	8.71	10.43	10.21	11.31	10.97	9.46	5.39	12.54	11.79	10.52	10.72	11.09	11.62	11.56	9.36	11.78	8.10	12.17	9.55	13.71	10.08	9.92	9.40	11.53	9.60	7.09
FPTLGGSQDKSLHN	9.38	8.53	9.12	7.79	9.22	9.24	8.54	9.20	8.54	10.61	8.43	9.45	9.39	9.18	10.14	8.99	10.94	9.76	9.49	9.86	10.48	9.77	9.86	10.53	11.02	8.61	10.98	9.65	10.26	9.90	10.67	8.76	10.18	8.77	10.34	9.16	9.20
TLGGSQDKSLHN	3.23	9.21	9.65	9.13	6.86	7.32	8.45	10.04	11.08	10.19	9.48	8.49	9.79	9.73	10.88	10.02	10.97	8.20	9.10	8.53	11.65	9.80	10.99	11.19	10.39	9.22	10.16	9.23	10.52	8.34	10.70	7.84	9.47	8.79	8.76	5.68	8.61
SVNPYLQGQRL	8.92	8.68	9.52	5.27	6.44	9.67	4.50	10.18	9.00	8.96	5.73	8.53	9.25	9.66	11.22	7.62	10.60	6.97	10.03	9.70	10.83	9.05	9.97	10.40	10.20	8.12	10.05	7.18	9.99	8.78	11.79	6.31	9.79	10.27	10.16	8.17	4.95
SVNPYLQGQRLDNVV	11.90	9.25	9.73	11.00	11.28	12.70	11.87	9.55	10.75	11.43	10.66	10.58	4.12	8.67	9.60	11.56	8.75	8.99	10.30	10.19	11.34	9.42	7.92	11.23	12.27	11.14	11.44	10.64	11.16	12.10	9.95	12.53	9.51	10.86	10.59	9.25	9.29
SVNPYLQGQRLDNVVA	11.40	9.34	9.39	10.53	11.03	11.59	11.30	9.49	10.04	11.59	10.16	10.59	9.05	8.66	10.78	10.69	10.07	9.28	10.14	9.84	11.65	9.93	8.66	11.88	11.96	10.39	11.52	10.34	11.04	11.63	10.31	11.70	10.43	10.36	10.59	8.42	9.23
SANSNPAM(+15.99)APRE	10.30	11.23	10.37	10.15	9.61	4.40	9.84	4.95	9.15	9.43	10.82	10.55	9.91	5.50	2.44	5.16	12.00	11.50	8.08	7.34	10.82	10.23	10.65	12.02	11.91	9.89	10.62	11.22	12.67	6.97	11.61	4.98	11.06	8.22	10.40	11.31	10.86
SANSNPAMAPRE	7.76	10.06	10.00	9.30	9.31	5.83	10.39	6.02	8.34	10.83	9.52	5.02	9.72	5.61	7.55	6.40	11.68	10.93	6.64	8.75	10.79	9.28	3.94	11.64	11.83	10.02	11.03	11.56	11.25	8.27	10.33	6.44	10.68	8.89	6.99	9.70	10.05

EigenMS normalization

After imputation using knn (k = 7), the data was normalized using EigenMS to account for sample-to-sample variability.

EigenMS normalization preserves the treatment group differences in the data by estimating treatment effects with an ANOVA model, then uses singular value decomposition on the model residual matrix to identify and remove the bias.

Code

plot_grid(hist_eigenms, qq_eigenms, pca_eigenms, nrow = 1)

Code

norm_d1_mod = norm_d1[-1,] %>%
        as.data.frame() %>%
        rownames_to_column(., var = "rowname") %>%
        mutate(across(-rowname, as.numeric)) %>%
        column_to_rownames(., var = "rowname")
#write.csv(norm_d1_mod, file = "after_norm_data.csv")

#rownames(norm_d1_mod) == feature_name$variable
rownames(norm_d1_mod) = feature_name$name

# display table
norm_d1_mod %>% 
        mutate(across(everything(), round, digit=2)) %>%
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

	Pituitary_53	Pituitary_31	Pituitary_38	Pituitary_63	Pituitary_55	Pituitary_51	Pituitary_50	Pituitary_34	Pituitary_59	Pituitary_43	Pituitary_66	Pituitary_26	Pituitary_19	Pituitary_24	Pituitary_41	Pituitary_57	Pituitary_47	Pituitary_52	Pituitary_23	Pituitary_58	Pituitary_44	Pituitary_37	Pituitary_39	Pituitary_46	Pituitary_65	Pituitary_56	Pituitary_48	Pituitary_35	Pituitary_61	Pituitary_49	Pituitary_60	Pituitary_54	Pituitary_45	Pituitary_42	Pituitary_62	Pituitary_25	Pituitary_64
AGAPEPAEPMELAKPSA	12.03	9.92	10.59	6.66	13.59	12.75	11.30	4.23	9.24	8.51	9.25	6.88	5.87	9.45	11.35	12.35	10.60	12.74	10.60	5.48	11.92	11.52	8.28	9.18	7.20	10.74	8.94	9.67	7.42	12.04	8.01	11.65	7.99	9.38	8.49	10.34	8.72
LAGAPEPA	8.74	8.21	11.22	7.57	10.60	11.67	10.90	8.25	5.13	8.47	7.36	8.96	8.93	9.75	9.28	13.71	7.93	12.96	7.11	6.94	3.42	10.97	6.13	6.70	4.96	12.27	5.28	9.74	7.79	11.91	6.93	11.21	5.78	6.42	6.62	9.56	6.13
AFGPRGPGLQL	9.41	8.75	9.50	10.25	10.05	8.95	10.09	9.84	5.16	10.93	9.56	9.36	9.49	9.49	10.30	9.34	8.80	8.27	9.02	9.16	10.07	8.75	9.14	10.24	10.00	9.55	10.10	9.61	9.78	9.40	10.00	11.15	9.76	11.03	9.74	7.76	10.62
AAMDLEL	10.02	5.12	9.15	8.77	12.37	4.89	9.73	8.42	9.16	9.86	9.13	8.67	9.42	8.39	10.08	8.06	8.92	7.61	7.92	8.71	8.24	10.39	7.90	9.86	6.63	9.10	10.09	7.72	9.65	9.35	11.95	10.82	9.62	8.36	8.73	8.86	8.48
AELDQLLHY	11.35	10.00	8.39	10.05	10.59	10.57	6.93	10.05	10.39	12.29	11.51	10.24	11.44	7.58	8.88	11.45	10.26	10.77	10.73	9.16	10.86	9.77	9.26	11.88	9.31	8.24	10.81	8.56	8.71	9.71	10.19	9.24	10.41	9.91	10.30	10.25	10.85
EDREEASLQDRQYASHHT	5.79	9.90	10.00	9.34	7.84	9.26	8.85	9.71	10.18	10.73	9.88	10.69	8.86	9.31	8.10	8.81	10.34	8.57	9.89	7.52	10.76	8.81	9.30	10.70	9.83	9.52	8.39	10.51	9.64	8.77	8.78	7.27	10.42	10.50	10.68	9.63	9.00
EDREEASLQDRQYASHHTTE	7.59	8.86	9.49	8.62	8.32	9.47	7.86	8.84	9.01	9.64	7.86	10.58	9.47	9.56	9.92	8.74	10.30	8.79	9.52	8.35	10.05	8.83	10.35	10.32	8.80	9.58	8.96	9.39	8.63	9.23	9.22	8.22	11.57	10.32	7.69	10.29	9.36
EEASLQDRQYASHHT	6.62	8.95	10.04	9.16	6.53	9.23	7.27	9.60	9.96	9.47	8.93	11.00	9.50	9.39	8.46	7.33	9.84	8.13	9.68	8.66	9.68	8.98	10.31	9.62	9.60	7.89	8.08	9.63	8.81	7.09	8.73	6.18	10.84	9.47	8.62	10.11	8.48
EEASLQDRQYASHHTTE	7.78	8.84	9.79	9.34	8.40	9.23	8.30	9.55	9.61	9.61	8.71	10.37	9.62	9.41	9.43	8.81	10.39	8.56	9.67	8.47	10.06	9.15	9.98	10.27	9.56	9.51	8.91	9.74	9.17	8.69	9.25	8.47	10.78	9.65	9.13	10.02	9.81
EESEESEEGTTSEVT	8.68	8.78	10.01	10.04	8.81	7.66	9.38	10.79	10.46	8.51	11.16	10.10	10.38	12.05	7.42	8.46	10.80	7.12	10.16	10.65	10.45	9.16	9.59	9.78	10.67	7.47	7.85	11.57	9.65	8.94	9.16	9.24	9.19	8.05	11.59	10.87	10.84
ELDQLLHY	10.41	10.35	9.90	10.52	10.17	8.96	9.37	9.70	10.68	10.09	10.87	9.38	11.37	9.32	10.87	9.56	10.14	7.92	10.04	9.67	10.26	9.40	9.59	10.64	10.38	8.74	10.83	10.06	9.42	6.36	8.52	8.79	9.83	7.24	11.49	8.27	10.62
FLGEAYHHVPE	9.69	7.94	9.43	8.38	8.91	8.75	8.50	8.74	6.19	10.75	8.37	9.27	10.08	9.17	10.19	9.98	8.75	8.91	9.97	9.46	8.82	9.85	9.57	10.30	8.69	7.11	9.47	8.07	8.86	8.65	8.80	6.79	9.99	11.03	7.18	10.58	9.29
FLGEAYHHVPES	9.45	8.86	9.87	9.44	9.46	8.61	9.58	10.22	8.27	10.70	10.05	10.31	10.17	8.91	9.70	9.11	9.35	9.90	10.27	10.04	9.43	9.93	8.67	9.37	8.90	6.60	8.98	8.81	9.71	8.38	8.33	7.77	9.92	9.00	9.40	9.57	8.90
FLGEAYHHVPESQ	9.08	9.09	9.76	9.22	9.62	6.16	9.40	10.38	8.14	10.72	8.97	10.16	9.59	9.65	9.48	9.27	9.54	8.11	10.32	9.94	9.38	9.01	8.20	10.67	9.41	7.55	9.71	9.61	10.06	6.20	8.87	8.97	10.05	9.98	10.01	9.38	9.16
FLGEAYHHVPESQRD	8.80	8.49	9.29	9.13	9.20	8.48	8.56	9.19	7.76	10.60	8.13	9.63	9.45	9.44	10.78	8.86	10.51	8.60	9.71	9.74	9.73	9.19	9.27	11.11	8.53	7.93	11.06	9.29	9.11	8.96	9.48	9.42	10.85	11.50	8.11	9.71	9.42
FLGEAYHHVPESQRDKA	6.34	8.71	9.37	10.77	8.46	8.05	9.22	9.44	8.26	10.80	8.34	9.48	9.13	9.34	9.91	9.19	10.66	8.14	9.90	9.10	9.82	10.63	9.27	11.60	8.40	8.14	10.50	9.30	9.35	8.72	9.90	9.26	11.37	9.88	9.86	10.20	10.53
GEAYHHVPESQRD	7.08	9.58	10.64	9.32	8.00	6.33	8.99	9.68	8.78	10.27	10.13	9.75	11.24	9.58	10.45	10.06	9.78	7.45	9.93	8.61	10.18	10.61	9.99	10.87	9.74	8.71	9.71	10.37	9.60	8.18	10.43	8.95	9.89	9.97	10.42	10.54	10.09
GEAYHHVPESQRDKA	4.07	8.91	9.59	10.47	8.03	7.69	8.81	8.87	8.77	10.32	8.45	10.26	10.61	8.85	10.36	9.36	10.37	7.57	9.03	8.12	9.44	11.28	10.60	11.27	8.73	7.48	9.86	8.76	9.27	8.09	10.33	8.16	10.97	9.73	9.50	9.85	10.57
GVLFNPYYDPLQWKSSRFE	12.04	9.65	9.99	10.13	10.85	9.38	11.15	8.50	9.32	11.34	9.19	9.34	11.52	8.25	9.90	12.20	10.73	9.45	10.78	8.90	11.05	10.93	9.88	12.18	9.65	11.50	10.85	9.43	11.70	9.98	10.74	12.84	9.43	12.16	10.60	9.42	10.34
LDQLLHY	8.70	9.65	9.54	9.12	9.43	7.88	8.90	10.63	10.23	11.99	9.59	8.87	10.85	9.20	10.45	9.11	9.85	8.82	9.98	9.69	10.67	10.38	9.93	11.04	9.75	7.34	10.80	9.74	9.37	7.77	9.43	8.77	10.33	10.65	10.36	9.62	10.62
LGEAYHHVPESQRD	8.32	8.88	9.23	9.97	8.51	4.69	8.80	9.49	7.77	11.79	8.60	9.19	9.13	9.38	10.25	9.29	10.58	7.91	9.68	9.02	10.28	9.23	8.11	11.37	8.35	6.73	11.41	9.65	9.14	7.73	9.29	9.87	10.64	10.72	9.61	10.10	7.29
LGVLFNPYYDPLQWKSSRFE	13.00	8.91	9.74	11.88	12.54	10.53	12.89	9.96	10.38	11.90	10.71	10.34	9.68	8.80	8.57	13.26	9.98	11.40	10.60	9.73	11.57	10.54	8.25	13.21	9.76	12.75	11.87	10.56	11.78	12.45	12.28	13.39	11.10	12.10	12.45	8.70	10.66
Q(-17.03)KIAEKFSQ	9.45	10.29	10.13	9.61	6.08	8.40	4.90	10.38	9.52	9.59	9.64	9.36	8.59	10.01	9.78	7.29	9.02	8.25	8.81	9.29	9.17	9.28	9.04	9.43	9.53	9.02	10.45	8.79	9.33	7.88	8.94	6.62	9.99	9.49	8.52	9.97	8.73
Q(-17.03)KIAEKFSQR(-.98)	4.91	9.13	9.29	7.98	4.80	7.82	4.31	9.23	9.30	9.45	8.06	9.95	8.80	9.14	10.07	7.68	10.62	7.92	8.40	9.22	10.25	9.71	10.11	10.22	8.79	10.01	10.74	8.59	8.36	8.58	9.58	7.05	11.07	11.04	7.20	11.32	9.47
Q(-17.03)YDRVAELDQLLHY	14.27	7.09	8.88	11.42	11.77	10.99	12.91	9.23	9.90	11.57	10.22	9.55	9.65	9.18	9.47	13.26	10.80	11.62	9.53	9.64	10.93	9.45	7.72	11.88	10.12	12.22	12.00	8.77	11.75	11.68	12.73	13.90	11.55	12.87	10.65	9.01	9.12
QYDRVAELDQLLHY	11.24	6.66	11.19	9.79	11.84	10.65	10.94	9.98	9.52	11.51	10.16	8.88	9.99	9.58	9.74	10.39	9.52	10.83	9.67	9.01	11.51	9.60	10.03	2.58	10.48	9.87	10.04	10.10	11.11	10.37	11.88	11.92	11.14	9.68	9.37	8.79	9.94
RVLTEEEEKELENL	11.51	10.70	10.73	9.60	10.24	11.18	11.39	10.56	10.24	9.89	10.20	9.83	10.47	11.12	10.82	8.98	8.79	9.39	10.66	11.42	9.73	9.86	10.74	8.93	9.44	10.60	11.03	10.59	10.65	10.47	12.11	8.25	10.75	11.51	9.01	10.81	9.30
SQGGEPGAYLTPDT	10.08	9.72	9.75	9.40	9.92	7.92	8.97	9.75	9.52	9.82	8.80	10.06	9.81	9.25	10.25	8.65	10.13	9.29	10.41	8.85	9.67	9.40	9.17	11.11	9.94	7.52	8.31	9.29	9.15	8.41	9.07	9.65	9.38	9.59	9.79	9.29	10.42
SQGGEPGAYLTPDTREE	9.05	8.78	9.17	9.20	10.16	8.56	9.32	8.84	9.59	10.23	9.18	9.55	9.82	9.44	9.41	9.17	10.01	9.05	10.06	9.87	9.38	9.11	8.75	10.27	9.20	7.77	10.19	8.81	8.80	8.81	8.95	9.34	9.57	9.34	9.59	9.03	10.16
SSQEGNPPSEERGHTLQEPEEAKVGE	8.47	9.05	9.26	9.67	10.11	9.51	10.10	9.74	9.19	10.07	9.17	10.40	9.61	10.35	9.86	10.70	10.74	9.98	10.83	9.18	10.55	9.46	9.89	10.91	9.76	10.10	10.57	10.16	8.78	10.30	8.91	10.14	11.27	9.49	9.78	11.08	10.23
VAELDQLLHY	10.36	10.70	9.74	10.43	10.78	10.45	10.90	9.92	10.65	7.60	10.81	10.23	9.93	8.99	10.45	10.49	9.31	9.73	9.74	9.20	10.81	9.70	9.41	12.12	9.70	9.06	10.82	10.68	10.49	9.81	10.49	11.24	9.89	10.06	11.15	8.73	10.38
YDRVAELDQLLHY	11.52	9.63	10.61	11.04	11.43	10.25	11.27	9.25	10.15	11.78	11.56	8.91	9.69	8.15	9.67	11.82	9.14	10.99	9.58	9.29	11.77	9.62	8.80	10.73	10.38	10.13	10.33	7.75	10.74	10.76	12.28	11.74	10.85	10.67	11.50	9.97	10.87
Q(-17.03)EPGAPAAGM	10.35	9.01	9.61	10.39	10.13	10.54	10.85	9.68	9.45	10.21	9.86	9.71	9.48	9.39	9.81	9.92	10.49	10.52	10.10	9.53	10.41	9.35	9.42	10.26	10.47	9.15	7.10	10.94	10.33	10.59	10.28	10.79	9.80	10.53	10.56	9.55	10.75
SLDSPAGPA	9.68	7.84	9.89	11.29	10.25	10.26	8.98	8.21	11.77	8.80	9.83	9.36	8.65	8.09	8.08	12.12	11.00	9.11	8.60	9.09	11.12	9.69	10.91	11.11	10.85	10.19	10.47	10.19	8.47	9.00	9.94	9.46	10.57	8.20	10.78	9.89	10.32
SLDSPAGPAE	7.16	7.35	10.10	8.96	9.84	9.22	7.43	8.82	11.98	7.81	8.07	10.25	7.13	9.72	8.90	5.73	10.75	7.95	6.21	9.21	10.14	9.54	12.02	10.92	9.71	7.75	9.85	7.94	8.05	8.43	9.75	8.31	10.64	10.33	7.55	9.02	8.61
VKVGVNGF	11.05	9.49	8.70	10.16	11.21	10.46	8.92	8.39	10.97	9.74	9.65	9.87	8.99	9.77	10.63	9.36	11.44	9.41	9.86	9.16	10.99	9.31	11.18	12.00	11.89	10.20	11.14	8.00	9.66	8.95	9.45	9.60	10.05	10.81	9.64	9.86	10.66
Q(-17.03)HWSYGLRPG(-.98)	10.03	8.08	8.76	8.68	8.77	8.32	9.28	9.43	9.06	10.71	8.99	7.58	7.58	9.36	9.80	8.63	9.88	8.76	7.50	9.29	10.00	7.40	5.17	9.55	7.74	8.88	9.87	8.37	10.07	9.66	9.61	8.21	9.59	11.04	9.29	8.45	8.10
SVSTVLTSKYR	9.10	9.96	9.59	9.63	11.00	10.59	8.43	8.91	9.97	9.88	10.16	9.67	7.97	10.30	8.39	7.97	11.62	8.60	9.69	10.54	10.00	9.44	10.57	11.12	10.26	8.68	10.54	6.71	8.12	9.43	9.83	9.14	9.83	9.89	9.36	10.40	11.54
GVANALSHKYH	7.82	10.35	9.42	8.18	9.37	8.57	8.45	8.32	9.57	10.94	9.21	11.01	7.62	10.66	9.14	8.93	13.10	9.24	8.54	9.66	9.75	9.49	8.46	11.01	9.39	9.98	7.67	9.44	8.07	9.77	8.37	9.02	10.94	10.24	9.66	5.40	11.66
KVVAGVANALSHKYH	10.63	10.13	8.90	10.11	10.56	9.73	8.52	8.95	10.65	11.41	10.27	10.55	9.87	10.19	10.27	10.20	11.87	10.51	10.73	10.08	11.01	10.95	10.69	11.27	10.24	10.19	10.59	8.73	10.77	10.82	10.43	10.34	11.07	11.50	9.63	10.62	10.88
VANALSHKYH	6.82	10.16	9.94	8.94	8.89	8.41	8.12	8.94	10.35	10.00	9.57	9.61	8.30	11.24	9.30	10.12	12.34	8.64	8.78	9.12	10.18	9.93	8.28	11.31	9.43	10.45	11.89	8.28	7.16	10.30	9.31	9.19	9.66	9.51	10.06	9.95	10.80
GRTLYGFGG	9.04	9.76	7.88	9.84	8.93	10.33	9.81	8.72	10.96	8.78	10.88	9.07	8.07	9.73	10.71	8.36	11.55	9.76	8.58	9.01	10.08	8.99	8.99	10.43	10.21	8.38	9.44	9.96	10.06	8.85	8.67	9.80	9.90	10.06	10.31	7.70	8.54
RTLYGFGG	8.94	9.64	7.53	10.04	9.30	10.19	9.09	8.68	11.24	9.58	10.73	8.83	7.92	9.84	10.56	8.25	11.62	9.51	8.68	9.09	10.04	9.14	9.49	10.19	10.67	8.64	9.42	9.86	10.23	8.42	9.34	9.46	9.92	10.46	10.32	8.07	9.19
TLYGFGG	10.40	10.47	10.04	10.00	10.92	12.31	11.63	8.47	12.04	9.87	10.69	6.80	10.59	8.28	12.55	11.14	9.08	10.19	9.47	9.04	9.03	10.04	11.66	9.67	11.17	8.39	11.68	9.99	11.29	8.73	10.21	9.61	9.57	11.41	10.27	8.82	9.98
AADQDLGPEAPPEGVLGA	10.70	8.85	8.19	9.71	11.15	9.59	11.33	10.55	9.03	10.15	9.68	8.30	10.18	7.87	10.22	10.66	10.24	9.61	10.15	9.27	10.35	9.57	9.81	10.21	9.30	10.84	10.48	9.89	9.46	10.57	9.19	10.85	10.06	8.62	10.54	9.55	10.44
AADQDLGPEAPPEGVLGAL	13.86	9.63	8.33	12.24	13.66	11.60	13.35	11.42	10.15	12.63	10.30	9.34	8.68	10.09	10.28	12.73	10.73	12.66	10.46	8.38	12.18	9.91	11.02	12.94	12.56	12.86	11.73	9.82	11.66	12.90	11.12	14.14	11.95	13.05	11.87	10.32	10.48
LENPQPQAPARRLLPP	10.27	8.56	8.87	9.43	9.59	9.71	9.61	8.14	7.39	9.39	9.42	10.16	9.37	9.55	10.99	10.56	9.35	10.48	9.08	9.40	9.68	8.91	9.37	9.74	9.42	10.00	9.29	8.73	9.56	11.04	9.68	9.63	10.47	10.33	7.94	9.74	8.82
VKMALQQEGFD	10.40	8.98	8.99	9.32	11.01	11.65	11.39	9.67	10.31	8.92	8.77	10.22	9.45	9.10	10.49	10.22	10.42	11.74	9.56	9.33	9.83	8.88	9.89	8.43	9.73	10.58	9.48	10.34	9.57	11.40	8.80	10.44	9.64	9.70	8.86	9.28	8.36
GGFMRGL	10.32	9.47	9.31	9.91	7.61	7.92	8.88	11.32	10.47	10.67	10.04	11.12	10.43	7.83	8.36	9.77	9.44	10.95	10.97	9.12	10.53	10.17	8.48	11.38	10.17	8.78	9.87	9.91	7.78	9.36	10.45	10.05	9.98	9.61	10.90	8.92	9.45
Q(-17.03)LEDEAKELQ	9.31	9.27	9.48	9.51	10.50	10.10	6.36	8.35	9.13	10.13	9.88	10.56	9.99	8.54	12.50	9.33	10.18	10.57	9.26	9.57	11.04	9.99	11.50	9.88	10.57	9.83	9.92	9.85	9.49	10.22	9.90	9.95	10.14	10.38	8.35	9.73	11.29
SPQLEDE	8.76	8.99	9.16	10.09	8.10	8.52	9.50	8.16	10.24	9.82	10.48	4.40	8.86	7.88	13.58	9.23	9.74	8.30	8.34	9.37	9.48	10.58	11.90	9.68	10.65	10.19	10.34	10.31	9.98	9.25	9.86	9.71	10.14	8.76	10.24	10.48	10.51
SPQLEDEAKEL	8.69	8.05	8.94	9.11	8.55	9.78	9.72	7.77	9.33	11.18	9.86	5.96	8.08	8.97	10.85	9.59	9.84	9.58	9.27	9.33	10.07	8.77	6.20	10.15	8.80	9.08	9.83	8.67	9.46	9.91	10.02	9.76	9.55	10.31	10.44	9.72	11.10
SPQLEDEAKELQ	7.62	8.61	9.13	9.45	9.88	9.60	8.70	7.43	8.88	10.07	9.53	10.23	9.36	8.37	9.51	8.93	9.59	9.32	10.02	9.23	9.68	9.57	10.78	9.69	9.95	8.61	9.48	8.69	8.95	9.09	9.08	8.50	9.65	9.62	8.90	9.10	9.90
VGRPEWWMDYQ	10.55	8.96	9.55	10.51	10.51	9.83	10.30	8.89	9.78	11.31	11.58	6.77	10.02	7.58	8.87	12.10	9.46	9.04	8.35	9.55	10.40	10.17	11.43	10.15	10.56	10.03	10.06	9.43	10.51	10.37	10.50	10.86	9.89	10.06	11.11	9.41	10.65
YGGFM(+15.99)RF	8.04	9.29	8.63	11.12	11.02	10.56	9.45	8.68	10.01	9.15	10.97	11.15	8.69	8.73	9.70	7.24	10.29	9.26	10.54	11.10	10.52	10.01	12.12	9.54	10.91	9.95	10.38	10.00	10.84	9.21	10.91	10.36	10.05	9.97	10.15	9.30	10.43
YGGFM(+15.99)RGL	8.32	9.67	9.45	10.92	11.12	8.84	9.15	7.68	9.97	9.93	11.03	11.08	9.30	8.44	8.90	12.50	10.52	9.87	10.43	10.68	10.14	10.30	11.85	10.54	11.10	10.05	10.44	10.22	10.34	9.37	10.80	10.32	10.71	9.98	10.48	10.14	10.70
YGGFMRF	9.41	7.74	9.04	8.62	9.21	8.86	9.37	8.17	8.63	10.46	9.57	6.77	8.70	8.13	10.57	8.73	9.42	8.56	8.44	9.46	8.87	7.98	6.59	9.92	8.41	9.23	10.10	7.86	9.38	8.77	9.12	9.40	8.73	9.51	9.52	8.67	9.49
YGGFMRGL	9.58	7.73	9.10	8.68	8.00	9.33	9.35	7.20	8.01	10.57	9.23	6.40	8.01	8.73	10.82	8.29	9.25	8.78	8.67	9.22	9.95	8.79	6.82	9.39	8.10	9.25	10.29	8.25	9.41	9.81	9.52	9.05	9.00	10.65	8.87	8.92	8.91
EIGDEENSAKFPI(-.98)	9.43	9.32	9.19	8.77	10.72	10.47	10.61	10.55	10.89	10.39	9.92	8.33	8.81	10.36	8.18	9.35	9.91	9.73	10.86	9.04	11.04	8.97	7.68	8.02	8.97	9.66	10.43	9.69	9.78	8.94	9.11	10.34	10.10	8.91	11.02	10.07	10.41
DDGPYRMEHFRWGSPPKD	9.53	9.77	10.13	8.69	10.35	10.41	11.22	9.39	9.01	11.86	9.40	9.34	10.10	9.03	10.32	9.86	10.39	11.09	9.79	9.11	10.73	10.25	9.59	9.60	7.45	11.06	9.25	10.21	8.91	12.23	7.89	9.99	10.32	9.14	9.26	9.92	8.01
FKNAIIKNAH	7.75	10.97	9.91	9.01	9.45	8.00	11.18	10.41	10.23	9.39	9.83	8.49	10.25	9.97	10.29	10.60	12.02	7.16	9.28	9.19	9.92	9.40	11.57	10.19	9.27	11.75	10.30	11.21	8.62	11.46	9.99	9.39	11.01	8.97	10.37	10.33	10.20
FKNAIIKNAHKKGQ	10.84	10.34	8.90	7.47	8.75	6.20	10.81	9.28	9.79	9.73	11.47	8.53	10.47	9.46	8.73	10.47	7.72	10.16	7.74	9.14	10.24	10.10	10.12	10.37	9.24	10.55	5.73	10.03	8.89	10.37	8.08	9.50	7.94	8.03	10.14	10.49	6.15
GGPEFRDDGAEPGPRE(-.98)	8.95	8.60	8.92	9.79	10.07	9.54	9.13	7.70	9.78	10.55	9.61	9.12	7.43	8.78	10.31	9.56	10.83	10.01	7.96	10.46	10.78	8.63	7.88	9.95	9.26	10.56	9.84	8.67	9.11	9.06	8.03	8.55	10.24	8.36	9.88	8.16	9.42
GPEFRDDGAEPGPRE(-.98)	9.13	8.95	9.07	9.91	10.00	9.80	9.15	7.77	9.80	10.60	10.19	8.73	6.98	8.73	10.26	9.98	10.93	9.70	8.18	9.50	11.26	8.88	8.21	10.68	10.00	10.53	10.27	9.05	10.07	9.09	8.87	8.66	9.89	10.36	10.33	8.57	9.30
KYVMGHFRWD	9.08	9.67	9.42	7.81	11.35	10.66	10.57	9.92	9.46	9.99	7.91	8.90	8.62	8.82	10.09	9.26	10.31	10.77	9.16	9.62	10.31	9.79	10.25	8.23	8.17	10.51	8.52	10.09	7.35	10.84	8.90	9.58	9.63	8.80	8.46	9.70	9.83
KYVMGHFRWDRF(-.98)	8.84	9.29	8.16	7.90	10.64	10.47	10.73	9.35	9.27	9.93	8.64	9.00	8.64	8.25	10.17	9.57	10.55	10.94	9.03	8.16	10.84	9.84	9.70	9.71	6.72	10.64	9.49	9.25	8.49	11.58	7.25	9.37	10.90	8.63	8.30	10.09	7.36
PEFRDDGAEPGPRE(-.98)	7.93	9.52	8.60	10.12	10.22	9.85	9.27	8.16	10.12	10.64	9.24	9.02	7.45	8.55	10.20	9.45	11.20	9.50	8.38	9.86	11.00	9.43	10.63	10.10	10.28	10.29	10.69	8.36	10.09	9.11	8.31	7.95	10.30	10.15	9.55	9.46	9.13
RPVKVYPNGAEDES(+79.97)AESFPLEF	13.73	9.42	9.62	9.05	10.38	11.95	13.33	10.00	9.86	0.60	9.34	9.48	7.84	8.22	10.04	13.09	8.02	11.21	8.60	10.00	8.94	8.76	8.57	8.87	10.24	10.97	9.97	10.04	10.60	11.49	10.11	12.22	8.58	8.48	9.23	7.96	10.02
RPVKVYPNGAEDESAESFPLEF	12.98	8.52	9.15	9.72	12.26	12.35	11.06	10.57	9.09	9.49	9.44	9.46	11.04	7.59	10.32	10.01	8.97	10.97	9.07	10.57	8.64	7.06	8.16	10.59	9.70	9.85	9.28	9.68	8.46	9.96	9.46	11.47	7.70	9.06	9.64	8.42	9.80
S(+42.01)YSMEHFRWGKPV(-.98)	10.87	9.28	9.77	8.82	10.72	10.99	11.03	9.08	8.54	10.37	7.99	9.59	8.94	9.07	10.58	9.53	10.17	11.34	8.93	10.22	9.52	9.13	10.64	9.69	7.66	10.46	9.97	9.68	8.65	11.45	7.66	10.37	10.79	9.91	7.21	10.01	6.35
SQTPLVTLF	11.46	10.70	10.47	11.78	11.29	10.86	11.30	10.57	9.99	10.37	11.34	9.57	10.21	9.36	10.33	9.22	9.45	9.58	9.83	9.90	10.18	8.26	9.60	8.72	11.67	8.71	11.90	11.30	10.22	10.16	9.33	11.49	9.30	9.44	12.12	5.12	10.80
SQTPLVTLFKNAIIKNAHKKGQ	7.03	9.41	8.24	10.67	10.55	10.92	9.28	8.69	9.66	13.77	10.62	7.03	7.33	5.26	7.83	9.61	10.33	10.28	10.29	10.05	10.94	9.16	10.08	11.78	9.26	9.21	10.08	9.50	10.04	8.75	7.78	10.32	10.28	10.06	11.86	9.82	10.28
SYSMEHF	8.22	9.05	10.15	10.02	10.17	10.04	9.41	10.25	9.74	10.28	10.28	9.73	9.03	9.55	10.35	8.39	10.28	9.90	9.62	10.08	10.47	9.54	10.00	10.28	10.89	8.05	9.59	10.93	9.77	9.47	10.02	10.75	9.59	11.00	10.56	9.16	11.12
SYSMEHFRWGKPV(-.98)	10.25	8.65	9.41	6.81	10.49	10.23	8.77	8.70	7.17	10.92	7.51	10.18	9.55	8.78	10.56	9.98	10.41	10.85	9.84	9.57	10.44	9.80	9.52	9.25	7.97	9.06	9.22	8.14	8.53	9.74	8.49	8.74	10.11	11.67	6.39	10.09	9.11
TPLVTLFKNAIIKNAHKKGQ	5.49	6.33	8.92	10.62	11.12	10.03	8.78	5.03	9.27	10.32	8.51	9.26	9.87	6.54	9.21	10.26	9.20	7.14	7.93	7.96	11.62	7.83	11.03	12.91	10.26	11.18	9.15	8.23	9.89	8.53	9.68	8.95	9.35	9.79	9.96	10.52	10.96
Y(+42.01)GGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAH	13.60	9.79	8.07	8.14	10.95	12.35	12.29	9.10	10.40	9.16	8.08	8.63	11.12	11.23	11.38	11.47	10.16	12.15	10.17	10.10	8.93	9.96	10.06	9.48	8.54	12.38	10.69	9.87	8.75	11.72	8.63	12.56	10.37	9.53	7.81	9.77	8.70
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNA	13.17	7.85	10.45	5.03	13.14	12.19	13.71	9.35	9.62	9.53	10.08	6.99	8.33	10.42	6.95	12.09	8.38	11.82	8.96	8.83	8.44	9.07	10.13	9.22	8.91	12.97	8.49	9.31	7.51	11.96	7.03	12.85	9.86	9.21	8.71	8.67	8.88
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	13.53	9.06	9.16	8.37	11.15	11.55	11.86	9.34	8.94	9.33	7.70	9.20	8.74	8.56	10.98	10.91	10.32	12.48	9.37	9.49	9.47	9.72	11.20	9.54	8.24	12.64	10.92	9.99	8.32	12.65	7.72	11.56	10.74	9.94	6.90	9.54	6.06
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	10.98	10.77	9.21	8.44	7.65	11.07	9.58	10.21	8.21	9.69	8.90	8.19	9.64	9.19	10.89	9.12	9.48	11.53	9.93	8.05	9.57	10.68	10.73	8.36	7.92	10.12	10.40	9.09	7.25	12.06	8.22	10.81	10.57	8.98	7.43	10.08	7.44
YGGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAHKKGQ	10.19	11.01	8.97	10.59	11.23	9.81	9.08	9.91	9.62	10.03	10.15	8.21	7.75	9.37	9.21	10.17	10.89	9.45	10.54	10.76	9.53	10.28	8.73	10.92	10.70	10.15	12.09	10.46	10.33	9.42	9.37	10.80	6.21	11.01	11.61	9.98	10.91
YGGFMTSE	9.50	8.95	9.81	10.40	10.61	10.33	9.85	10.29	9.29	11.65	9.88	8.99	9.42	9.95	10.04	9.32	9.96	10.51	10.10	9.58	10.46	9.87	9.78	9.93	10.74	8.43	11.22	11.05	9.39	10.27	9.32	11.74	9.38	11.09	10.69	8.74	10.61
YGGFMTSEKSQTPLVTLFKNAIIKNA	11.31	10.04	9.86	11.01	11.95	11.57	11.61	10.58	10.42	11.26	10.33	10.11	8.48	8.73	10.33	12.60	10.30	13.05	11.12	9.42	11.72	10.81	9.86	10.67	11.61	12.32	11.20	10.74	11.08	11.50	10.86	11.98	10.08	11.86	11.49	10.66	10.53
YGGFMTSEKSQTPLVTLFKNAIIKNAH	9.74	10.83	10.42	10.11	11.13	10.72	10.24	10.06	9.15	10.09	8.50	8.96	10.34	8.99	10.71	11.76	7.11	11.70	9.62	8.30	10.52	10.11	10.50	7.74	10.21	10.66	9.29	10.92	10.00	10.36	9.54	11.17	8.29	9.35	9.90	10.67	9.92
YGGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	9.08	9.87	9.57	9.78	10.70	9.72	9.28	10.52	10.41	10.68	10.38	9.70	10.52	9.23	9.92	9.16	10.16	9.16	9.45	9.37	10.31	9.67	9.49	10.76	9.00	9.43	11.31	9.23	9.18	9.12	9.23	9.98	10.22	8.80	10.50	9.24	10.15
ATLESVFQELGKLTGPSSQKRE	11.86	10.14	9.76	11.32	10.20	11.39	10.67	9.42	10.27	11.08	11.41	11.01	11.84	8.15	11.36	9.67	10.10	11.00	11.83	10.28	10.41	11.82	9.91	11.39	10.91	7.84	10.99	6.70	10.32	7.80	12.13	9.09	9.79	10.65	10.39	10.13	10.66
MYEENSRDNPF	8.81	9.00	9.68	9.45	9.51	9.35	9.51	9.54	10.29	10.08	9.57	9.95	10.01	9.22	10.04	8.03	10.07	9.27	10.04	9.05	9.83	9.58	10.14	9.42	10.38	7.96	9.21	9.96	10.12	8.44	10.38	9.84	9.37	11.11	9.65	9.06	9.47
TNEIVEEQYTPQSL	11.93	10.78	11.78	10.97	10.11	10.00	9.82	9.50	11.55	11.06	9.85	8.90	11.40	9.64	10.11	9.43	10.01	7.59	10.78	10.45	9.95	10.14	11.01	10.71	9.99	10.19	12.53	9.12	11.26	8.23	12.16	9.51	9.99	11.42	10.17	10.97	9.78
FPTLGGSQDKSLHN	9.39	8.34	9.08	9.42	9.28	8.70	8.94	9.43	9.31	10.32	9.50	9.59	9.37	9.01	10.40	9.13	10.58	9.38	9.68	9.76	10.54	9.80	9.70	9.94	10.11	9.13	10.55	9.47	9.23	9.51	9.48	8.93	10.06	10.24	9.41	9.32	9.89
TLGGSQDKSLHN	4.15	9.63	9.24	9.25	6.84	7.13	8.97	8.97	11.01	9.99	9.55	9.76	10.10	8.81	10.78	9.12	10.79	7.86	7.44	8.11	10.55	10.42	10.41	10.02	10.29	9.29	10.48	9.68	9.56	8.21	9.50	7.92	10.46	10.22	10.39	7.25	9.53
SVNPYLQGQRL	9.56	9.13	9.30	7.66	6.05	8.24	6.46	9.64	9.92	9.01	7.88	9.35	9.39	8.79	10.51	6.71	10.55	7.48	8.62	8.51	10.48	8.94	9.32	9.52	9.12	8.77	10.50	8.22	9.01	7.74	9.90	6.34	9.56	11.99	7.13	9.53	7.65
SVNPYLQGQRLDNVV	11.80	9.16	10.22	11.75	11.79	11.82	11.58	9.17	9.83	10.10	10.67	9.22	5.50	9.12	8.75	10.68	9.60	11.57	10.14	9.94	11.31	8.72	8.51	11.21	11.39	11.74	11.66	10.62	10.99	11.46	10.10	11.64	9.82	11.70	11.70	9.05	9.49
SVNPYLQGQRLDNVVA	11.48	9.09	9.61	11.33	11.05	10.94	11.37	9.36	9.82	10.93	10.51	10.17	9.55	8.96	10.54	10.36	10.42	10.63	10.05	9.59	11.62	9.31	9.31	11.66	10.80	10.82	11.59	10.21	10.69	11.10	10.05	11.28	10.31	11.22	11.14	8.39	9.75
SANSNPAM(+15.99)APRE	9.53	9.52	10.10	10.89	9.40	5.78	8.35	7.24	11.31	9.96	10.97	11.41	7.66	6.31	5.69	8.40	10.01	7.01	11.40	9.13	11.75	10.58	11.54	11.56	10.53	9.92	8.24	8.64	11.14	7.86	10.71	6.40	10.04	9.36	11.44	9.60	8.78
SANSNPAMAPRE	8.03	8.08	9.65	9.23	8.10	6.83	9.37	7.41	9.75	11.41	9.30	6.97	7.32	6.66	10.67	8.98	10.23	8.19	8.53	9.77	10.95	8.45	6.50	10.74	8.70	9.85	9.60	9.14	10.02	8.63	9.62	7.37	9.29	10.19	10.77	8.86	9.18

Peak intensity plots

EigenMS removes sample-to-sample variability.

Intensity after log2 transformation

Intensity after EigenMS normalization

Univariate analysis

Univariate statistic analysis will proceed for each pairs of comparison. For each pair,

Step 1, differential analysis;

• t-test

• Wilcoxon rank-sum test

For all statistical tests, the Benjamini-Hochberg (BH) procedure was applied to correct for multiple hypothesis testing.

Step 2, fold change, both linear and log2;

Step 3, regulation shown in volcano plot.

• A feature is considered unregulated when FC(log2) > 0.6 (or FC(lin) > 1.5);

• A feature is considered downregulated when FC(log2) < -0.6 (or FC(lin) < -1.5).

Code

d5 <- rbind.data.frame(labels_d1, norm_d1_mod) 
d5_mod <- t(d5) %>%
  as.data.frame(.) %>%
  rownames_to_column(., var = "rowname") %>%
  as_tibble() %>%
  dplyr::rename(., Label = class) %>%
  mutate(across(-c(Label,rowname), as.numeric)) %>%
  #rename_with(str_trim)
  column_to_rownames(., var = "rowname")

#colnames(d5_mod)[-1] == feature_name$variable
colnames(d5_mod)[-1] = feature_name$name

grps = as.factor(t(labels_d1))
trt= levels(grps)

combo_list = do.call("c", lapply(seq_along(time), function(i) combn(trt, 2, FUN = list))) # top 10 are unique combo
#combo_list = combo_list[1:10]

feature_meta = read.csv(file = "feature_meta_pituitary.csv")

folder = paste(getwd(), "/pituitary/", sep = "")

August vs IBA

Full stat

Code

contrast = combo_list[[1]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: August over IBA"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
AADQDLGPEAPPEGVLGA	0.012	0.035	0.012	0.035	0.482	-1.053	0.035	1.454	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.000	0.001	0.000	0.003	0.119	-3.072	0.001	2.966	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AAMDLEL	0.592	0.704	0.456	0.579	0.430	-1.218	0.579	0.237	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AELDQLLHY	0.561	0.676	0.529	0.654	0.635	-0.654	0.654	0.184	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AFGPRGPGLQL	0.134	0.233	0.224	0.351	0.609	-0.716	0.233	0.633	tr|I3MMW2|I3MMW2_ICTTR	Chromogranin-A	CHGA
AGAPEPAEPMELAKPSA	0.005	0.019	0.002	0.008	0.269	-1.893	0.008	2.102	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
ATLESVFQELGKLTGPSSQKRE	0.934	0.954	0.955	0.955	1.184	0.244	0.954	0.021	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-2	SCG2
DDGPYRMEHFRWGSPPKD	0.053	0.122	0.113	0.213	0.546	-0.872	0.122	0.915	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
EDREEASLQDRQYASHHT	0.010	0.030	0.008	0.025	2.267	1.181	0.025	1.609	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EDREEASLQDRQYASHHTTE	0.011	0.031	0.018	0.047	1.935	0.952	0.031	1.503	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHT	0.000	0.001	0.001	0.006	4.550	2.186	0.001	3.194	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHTTE	0.000	0.002	0.002	0.008	2.043	1.030	0.002	2.626	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EESEESEEGTTSEVT	0.002	0.011	0.002	0.008	3.628	1.859	0.008	2.102	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EIGDEENSAKFPI(-.98)	0.331	0.472	0.456	0.579	0.799	-0.323	0.472	0.326	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
ELDQLLHY	0.229	0.341	0.328	0.467	1.289	0.367	0.341	0.467	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FKNAIIKNAH	0.366	0.514	0.607	0.713	1.108	0.148	0.514	0.289	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FKNAIIKNAHKKGQ	0.795	0.839	0.328	0.467	0.790	-0.340	0.467	0.331	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FLGEAYHHVPE	0.065	0.139	0.113	0.213	1.831	0.872	0.139	0.857	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPES	0.108	0.198	0.113	0.213	1.515	0.599	0.198	0.702	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQ	0.059	0.128	0.088	0.188	1.770	0.824	0.128	0.893	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.003	0.012	0.008	0.025	1.530	0.613	0.012	1.924	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRDKA	0.003	0.013	0.000	0.003	2.422	1.276	0.003	2.467	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FPTLGGSQDKSLHN	0.031	0.082	0.050	0.119	1.278	0.353	0.082	1.089	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-3	SCG3
GEAYHHVPESQRD	0.000	0.003	0.002	0.008	3.477	1.798	0.003	2.580	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GEAYHHVPESQRDKA	0.005	0.019	0.003	0.011	3.990	1.996	0.011	1.942	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GGFMRGL	0.533	0.658	0.607	0.713	1.167	0.223	0.658	0.181	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GGPEFRDDGAEPGPRE(-.98)	0.001	0.007	0.003	0.011	0.437	-1.195	0.007	2.138	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GPEFRDDGAEPGPRE(-.98)	0.004	0.017	0.003	0.011	0.514	-0.961	0.011	1.942	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GRTLYGFGG	0.197	0.313	0.328	0.467	0.699	-0.516	0.313	0.504	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
GVANALSHKYH	0.441	0.583	0.864	0.902	0.840	-0.251	0.583	0.235	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
GVLFNPYYDPLQWKSSRFE	0.070	0.146	0.145	0.252	0.412	-1.280	0.146	0.836	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
KVVAGVANALSHKYH	0.893	0.933	0.456	0.579	1.042	0.059	0.579	0.237	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
KYVMGHFRWD	0.097	0.188	0.181	0.304	0.623	-0.682	0.188	0.727	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
KYVMGHFRWDRF(-.98)	0.035	0.088	0.066	0.152	0.483	-1.051	0.088	1.055	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
LAGAPEPA	0.036	0.090	0.036	0.089	0.235	-2.089	0.089	1.051	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
LDQLLHY	0.000	0.003	0.000	0.003	2.350	1.233	0.003	2.580	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LENPQPQAPARRLLPP	0.001	0.006	0.005	0.018	0.491	-1.025	0.006	2.224	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGEAYHHVPESQRD	0.039	0.092	0.066	0.152	1.922	0.943	0.092	1.036	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LGVLFNPYYDPLQWKSSRFE	0.000	0.003	0.003	0.011	0.156	-2.680	0.003	2.580	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
MYEENSRDNPF	0.016	0.045	0.018	0.047	1.605	0.682	0.045	1.346	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-3	SCG2
PEFRDDGAEPGPRE(-.98)	0.758	0.829	0.776	0.848	0.935	-0.097	0.829	0.082	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Q(-17.03)EPGAPAAGM	0.141	0.236	0.181	0.304	0.737	-0.440	0.236	0.627	tr|I3MIV6|I3MIV6_ICTTR	Carboxypeptidase E	CPE
Q(-17.03)HWSYGLRPG(-.98)	0.055	0.123	0.018	0.047	0.466	-1.103	0.047	1.326	tr|I3MCA0|I3MCA0_ICTTR	Progonadoliberin-1	GNRH1
Q(-17.03)KIAEKFSQ	0.007	0.022	0.012	0.035	2.551	1.351	0.022	1.652	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)KIAEKFSQR(-.98)	0.006	0.021	0.008	0.025	3.821	1.934	0.021	1.683	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)LEDEAKELQ	0.474	0.611	0.864	0.902	1.237	0.307	0.611	0.214	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
Q(-17.03)YDRVAELDQLLHY	0.000	0.000	0.000	0.003	0.066	-3.912	0.000	3.769	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
QYDRVAELDQLLHY	0.030	0.081	0.026	0.067	0.516	-0.956	0.067	1.175	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPVKVYPNGAEDES(+79.97)AESFPLEF	0.000	0.001	0.000	0.003	0.099	-3.337	0.001	3.194	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RPVKVYPNGAEDESAESFPLEF	0.000	0.003	0.000	0.003	0.143	-2.801	0.003	2.580	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RTLYGFGG	0.494	0.627	0.689	0.771	0.867	-0.206	0.627	0.202	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
RVLTEEEEKELENL	0.416	0.559	0.607	0.713	1.027	0.039	0.559	0.253	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
S(+42.01)YSMEHFRWGKPV(-.98)	0.007	0.022	0.012	0.035	0.486	-1.041	0.022	1.652	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SANSNPAM(+15.99)APRE	0.005	0.019	0.005	0.018	4.009	2.003	0.018	1.744	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SANSNPAMAPRE	0.790	0.839	0.689	0.771	1.103	0.142	0.771	0.113	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SLDSPAGPA	0.938	0.954	0.955	0.955	0.832	-0.265	0.954	0.021	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SLDSPAGPAE	0.236	0.346	0.224	0.351	3.406	1.768	0.346	0.460	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SPQLEDE	0.096	0.188	0.088	0.188	2.513	1.329	0.188	0.727	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKEL	0.176	0.286	0.145	0.252	0.671	-0.575	0.252	0.599	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.129	0.228	0.145	0.252	1.600	0.678	0.228	0.641	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SQGGEPGAYLTPDT	0.104	0.195	0.224	0.351	1.377	0.462	0.195	0.710	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQGGEPGAYLTPDTREE	0.666	0.764	0.955	0.955	1.055	0.078	0.764	0.117	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQTPLVTLF	0.204	0.320	0.272	0.406	0.577	-0.794	0.320	0.495	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SQTPLVTLFKNAIIKNAHKKGQ	0.944	0.954	0.689	0.771	0.853	-0.230	0.771	0.113	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SSQEGNPPSEERGHTLQEPEEAKVGE	0.640	0.742	0.864	0.902	1.171	0.228	0.742	0.129	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SVNPYLQGQRL	0.006	0.021	0.036	0.089	2.152	1.106	0.021	1.683	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B2	SCG5
SVNPYLQGQRLDNVV	0.002	0.009	0.000	0.003	0.281	-1.833	0.003	2.467	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B3	SCG5
SVNPYLQGQRLDNVVA	0.001	0.007	0.000	0.003	0.366	-1.448	0.003	2.467	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B4	SCG5
SVSTVLTSKYR	0.786	0.839	0.388	0.529	1.166	0.221	0.529	0.276	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SYSMEHF	0.219	0.332	0.388	0.529	1.302	0.380	0.332	0.479	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SYSMEHFRWGKPV(-.98)	0.414	0.559	0.388	0.529	0.769	-0.379	0.529	0.276	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
TLGGSQDKSLHN	0.110	0.199	0.113	0.213	2.468	1.303	0.199	0.701	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-4	SCG3
TLYGFGG	0.539	0.658	0.529	0.654	0.684	-0.548	0.654	0.184	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TNEIVEEQYTPQSL	0.098	0.188	0.113	0.213	1.656	0.728	0.188	0.727	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-4	SCG2
TPLVTLFKNAIIKNAHKKGQ	0.978	0.978	0.776	0.848	0.869	-0.203	0.848	0.072	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
VAELDQLLHY	0.084	0.171	0.088	0.188	0.633	-0.659	0.171	0.766	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
VANALSHKYH	0.708	0.783	0.955	0.955	1.007	0.010	0.783	0.106	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
VGRPEWWMDYQ	0.209	0.322	0.145	0.252	0.668	-0.582	0.252	0.599	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.000	0.003	0.001	0.006	0.353	-1.501	0.003	2.580	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGF	0.446	0.583	0.456	0.579	0.808	-0.307	0.579	0.237	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
Y(+42.01)GGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAH	0.000	0.001	0.000	0.003	0.170	-2.554	0.001	2.857	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNA	0.000	0.000	0.000	0.003	0.108	-3.208	0.000	3.769	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	0.000	0.002	0.002	0.008	0.209	-2.255	0.002	2.654	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.502	0.629	0.272	0.406	0.619	-0.692	0.406	0.391	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YDRVAELDQLLHY	0.006	0.021	0.002	0.008	0.336	-1.574	0.008	2.102	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
YGGFM(+15.99)RF	0.329	0.472	0.456	0.579	1.650	0.723	0.472	0.326	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)RGL	0.411	0.559	0.272	0.406	1.058	0.081	0.406	0.391	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAHKKGQ	0.612	0.720	0.864	0.902	0.871	-0.199	0.720	0.143	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMRF	0.039	0.092	0.008	0.025	0.569	-0.815	0.025	1.609	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.150	0.247	0.113	0.213	0.674	-0.569	0.213	0.671	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMTSE	0.704	0.783	0.689	0.771	0.823	-0.281	0.771	0.113	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNA	0.000	0.003	0.000	0.003	0.350	-1.513	0.003	2.580	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAH	0.139	0.236	0.224	0.351	0.688	-0.539	0.236	0.627	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.707	0.783	0.607	0.713	0.889	-0.169	0.713	0.147	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	status	Accession	Name	GN
AADQDLGPEAPPEGVLGA	0.012	0.035	0.012	0.035	0.482	-1.053	0.035	1.454	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.000	0.001	0.000	0.003	0.119	-3.072	0.001	2.966	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AGAPEPAEPMELAKPSA	0.005	0.019	0.002	0.008	0.269	-1.893	0.008	2.102	Down	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
EDREEASLQDRQYASHHT	0.010	0.030	0.008	0.025	2.267	1.181	0.025	1.609	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EDREEASLQDRQYASHHTTE	0.011	0.031	0.018	0.047	1.935	0.952	0.031	1.503	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHT	0.000	0.001	0.001	0.006	4.550	2.186	0.001	3.194	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHTTE	0.000	0.002	0.002	0.008	2.043	1.030	0.002	2.626	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EESEESEEGTTSEVT	0.002	0.011	0.002	0.008	3.628	1.859	0.008	2.102	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.003	0.012	0.008	0.025	1.530	0.613	0.012	1.924	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRDKA	0.003	0.013	0.000	0.003	2.422	1.276	0.003	2.467	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GEAYHHVPESQRD	0.000	0.003	0.002	0.008	3.477	1.798	0.003	2.580	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GEAYHHVPESQRDKA	0.005	0.019	0.003	0.011	3.990	1.996	0.011	1.942	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GGPEFRDDGAEPGPRE(-.98)	0.001	0.007	0.003	0.011	0.437	-1.195	0.007	2.138	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GPEFRDDGAEPGPRE(-.98)	0.004	0.017	0.003	0.011	0.514	-0.961	0.011	1.942	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
LDQLLHY	0.000	0.003	0.000	0.003	2.350	1.233	0.003	2.580	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LENPQPQAPARRLLPP	0.001	0.006	0.005	0.018	0.491	-1.025	0.006	2.224	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGVLFNPYYDPLQWKSSRFE	0.000	0.003	0.003	0.011	0.156	-2.680	0.003	2.580	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
MYEENSRDNPF	0.016	0.045	0.018	0.047	1.605	0.682	0.045	1.346	Up	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-3	SCG2
Q(-17.03)KIAEKFSQ	0.007	0.022	0.012	0.035	2.551	1.351	0.022	1.652	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)KIAEKFSQR(-.98)	0.006	0.021	0.008	0.025	3.821	1.934	0.021	1.683	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)YDRVAELDQLLHY	0.000	0.000	0.000	0.003	0.066	-3.912	0.000	3.769	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPVKVYPNGAEDES(+79.97)AESFPLEF	0.000	0.001	0.000	0.003	0.099	-3.337	0.001	3.194	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RPVKVYPNGAEDESAESFPLEF	0.000	0.003	0.000	0.003	0.143	-2.801	0.003	2.580	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
S(+42.01)YSMEHFRWGKPV(-.98)	0.007	0.022	0.012	0.035	0.486	-1.041	0.022	1.652	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SANSNPAM(+15.99)APRE	0.005	0.019	0.005	0.018	4.009	2.003	0.018	1.744	Up	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SVNPYLQGQRLDNVV	0.002	0.009	0.000	0.003	0.281	-1.833	0.003	2.467	Down	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B3	SCG5
SVNPYLQGQRLDNVVA	0.001	0.007	0.000	0.003	0.366	-1.448	0.003	2.467	Down	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B4	SCG5
VKMALQQEGFD	0.000	0.003	0.001	0.006	0.353	-1.501	0.003	2.580	Down	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
Y(+42.01)GGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAH	0.000	0.001	0.000	0.003	0.170	-2.554	0.001	2.857	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNA	0.000	0.000	0.000	0.003	0.108	-3.208	0.000	3.769	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	0.000	0.002	0.002	0.008	0.209	-2.255	0.002	2.654	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YDRVAELDQLLHY	0.006	0.021	0.002	0.008	0.336	-1.574	0.008	2.102	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
YGGFMTSEKSQTPLVTLFKNAIIKNA	0.000	0.003	0.000	0.003	0.350	-1.513	0.003	2.580	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

August vs March

Full stat

Code

contrast = combo_list[[2]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: August over March"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
AADQDLGPEAPPEGVLGA	0.078	0.127	0.036	0.070	0.674	-0.570	0.070	1.152	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.021	0.048	0.036	0.070	0.482	-1.053	0.048	1.321	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AAMDLEL	0.727	0.781	0.743	0.785	0.624	-0.680	0.781	0.107	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AELDQLLHY	0.229	0.296	0.370	0.446	1.533	0.617	0.296	0.529	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AFGPRGPGLQL	0.136	0.196	0.093	0.141	1.409	0.495	0.141	0.852	tr|I3MMW2|I3MMW2_ICTTR	Chromogranin-A	CHGA
AGAPEPAEPMELAKPSA	0.001	0.006	0.002	0.006	0.248	-2.011	0.006	2.213	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
ATLESVFQELGKLTGPSSQKRE	0.174	0.241	0.370	0.446	1.245	0.316	0.241	0.619	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-2	SCG2
DDGPYRMEHFRWGSPPKD	0.317	0.382	0.277	0.356	0.752	-0.412	0.356	0.448	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
EDREEASLQDRQYASHHT	0.007	0.021	0.021	0.047	3.147	1.654	0.021	1.677	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EDREEASLQDRQYASHHTTE	0.001	0.004	0.001	0.003	2.874	1.523	0.003	2.545	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHT	0.000	0.002	0.001	0.003	3.938	1.978	0.002	2.680	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHTTE	0.000	0.003	0.001	0.003	2.415	1.272	0.003	2.545	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EESEESEEGTTSEVT	0.278	0.348	0.423	0.498	1.832	0.873	0.348	0.459	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EIGDEENSAKFPI(-.98)	0.522	0.577	0.673	0.727	0.940	-0.089	0.577	0.239	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
ELDQLLHY	0.086	0.138	0.046	0.079	1.957	0.969	0.079	1.101	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FKNAIIKNAH	0.364	0.417	0.606	0.670	1.116	0.158	0.417	0.380	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FKNAIIKNAHKKGQ	0.133	0.195	0.046	0.079	0.503	-0.991	0.079	1.101	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FLGEAYHHVPE	0.011	0.027	0.011	0.029	2.349	1.232	0.027	1.563	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPES	0.071	0.119	0.236	0.308	1.548	0.631	0.119	0.923	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQ	0.006	0.018	0.001	0.004	2.518	1.332	0.004	2.355	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.000	0.000	0.000	0.001	4.087	2.031	0.000	4.650	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRDKA	0.000	0.001	0.000	0.001	4.343	2.119	0.001	3.141	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FPTLGGSQDKSLHN	0.000	0.000	0.000	0.001	2.250	1.170	0.000	5.140	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-3	SCG3
GEAYHHVPESQRD	0.001	0.004	0.001	0.004	3.056	1.611	0.004	2.423	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GEAYHHVPESQRDKA	0.001	0.004	0.000	0.001	4.852	2.279	0.001	3.066	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GGFMRGL	0.179	0.245	0.236	0.308	1.491	0.576	0.245	0.612	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GGPEFRDDGAEPGPRE(-.98)	0.101	0.154	0.093	0.141	1.558	0.640	0.141	0.852	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GPEFRDDGAEPGPRE(-.98)	0.002	0.006	0.002	0.009	1.895	0.923	0.006	2.209	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GRTLYGFGG	0.036	0.072	0.036	0.070	1.904	0.929	0.070	1.152	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
GVANALSHKYH	0.055	0.102	0.046	0.079	3.878	1.955	0.079	1.101	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
GVLFNPYYDPLQWKSSRFE	0.873	0.922	0.815	0.851	0.839	-0.253	0.851	0.070	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
KVVAGVANALSHKYH	0.006	0.018	0.004	0.012	1.886	0.916	0.012	1.936	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
KYVMGHFRWD	0.061	0.108	0.046	0.079	0.580	-0.787	0.079	1.101	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
KYVMGHFRWDRF(-.98)	0.489	0.553	0.541	0.606	0.794	-0.333	0.553	0.257	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
LAGAPEPA	0.000	0.001	0.000	0.001	0.043	-4.541	0.001	3.141	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
LDQLLHY	0.000	0.000	0.000	0.001	4.580	2.195	0.000	3.902	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LENPQPQAPARRLLPP	0.499	0.559	0.423	0.498	0.898	-0.156	0.498	0.303	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGEAYHHVPESQRD	0.000	0.002	0.000	0.001	5.558	2.475	0.001	3.066	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LGVLFNPYYDPLQWKSSRFE	0.070	0.119	0.059	0.098	0.536	-0.901	0.098	1.010	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
MYEENSRDNPF	0.010	0.026	0.021	0.047	1.880	0.911	0.026	1.581	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-3	SCG2
PEFRDDGAEPGPRE(-.98)	0.002	0.009	0.002	0.009	2.148	1.103	0.009	2.066	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Q(-17.03)EPGAPAAGM	0.294	0.363	0.167	0.238	0.804	-0.316	0.238	0.623	tr|I3MIV6|I3MIV6_ICTTR	Carboxypeptidase E	CPE
Q(-17.03)HWSYGLRPG(-.98)	0.001	0.005	0.006	0.015	2.119	1.084	0.005	2.268	tr|I3MCA0|I3MCA0_ICTTR	Progonadoliberin-1	GNRH1
Q(-17.03)KIAEKFSQ	0.003	0.010	0.001	0.003	3.025	1.597	0.003	2.545	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)KIAEKFSQR(-.98)	0.001	0.004	0.000	0.001	5.746	2.523	0.001	2.890	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)LEDEAKELQ	0.095	0.147	0.167	0.238	1.922	0.942	0.147	0.833	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
Q(-17.03)YDRVAELDQLLHY	0.045	0.087	0.046	0.079	0.418	-1.258	0.079	1.101	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
QYDRVAELDQLLHY	0.214	0.283	0.167	0.238	0.688	-0.540	0.238	0.623	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPVKVYPNGAEDES(+79.97)AESFPLEF	0.006	0.019	0.000	0.001	0.091	-3.466	0.001	3.066	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RPVKVYPNGAEDESAESFPLEF	0.001	0.006	0.002	0.009	0.232	-2.109	0.006	2.213	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RTLYGFGG	0.003	0.010	0.004	0.012	2.269	1.182	0.010	1.987	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
RVLTEEEEKELENL	0.936	0.966	0.888	0.898	0.933	-0.100	0.898	0.047	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
S(+42.01)YSMEHFRWGKPV(-.98)	0.023	0.052	0.021	0.047	0.633	-0.661	0.047	1.325	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SANSNPAM(+15.99)APRE	0.095	0.147	0.074	0.119	3.343	1.741	0.119	0.926	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SANSNPAMAPRE	0.000	0.002	0.001	0.003	3.701	1.888	0.002	2.796	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SLDSPAGPA	0.968	0.978	0.743	0.785	1.050	0.071	0.785	0.105	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SLDSPAGPAE	0.003	0.010	0.004	0.012	3.484	1.801	0.010	1.987	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SPQLEDE	0.073	0.120	0.036	0.070	3.874	1.954	0.070	1.152	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKEL	0.007	0.019	0.006	0.015	1.794	0.843	0.015	1.817	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.010	0.026	0.011	0.029	1.542	0.625	0.026	1.581	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SQGGEPGAYLTPDT	0.056	0.102	0.074	0.119	1.755	0.812	0.102	0.990	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQGGEPGAYLTPDTREE	0.010	0.026	0.002	0.009	1.626	0.701	0.009	2.066	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQTPLVTLF	0.335	0.394	0.481	0.544	0.728	-0.458	0.394	0.404	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SQTPLVTLFKNAIIKNAHKKGQ	0.155	0.221	0.200	0.272	3.215	1.685	0.221	0.656	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SSQEGNPPSEERGHTLQEPEEAKVGE	0.113	0.168	0.236	0.308	1.409	0.494	0.168	0.774	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SVNPYLQGQRL	0.000	0.001	0.001	0.003	6.020	2.590	0.001	3.031	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B2	SCG5
SVNPYLQGQRLDNVV	0.032	0.068	0.021	0.047	0.593	-0.755	0.047	1.325	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B3	SCG5
SVNPYLQGQRLDNVVA	0.893	0.932	0.888	0.898	1.062	0.087	0.898	0.047	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B4	SCG5
SVSTVLTSKYR	0.067	0.117	0.093	0.141	1.829	0.871	0.117	0.932	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SYSMEHF	0.035	0.071	0.027	0.060	1.578	0.658	0.060	1.223	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SYSMEHFRWGKPV(-.98)	0.188	0.252	0.167	0.238	1.477	0.562	0.238	0.623	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
TLGGSQDKSLHN	0.001	0.004	0.000	0.001	4.597	2.201	0.001	3.066	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-4	SCG3
TLYGFGG	0.984	0.984	1.000	1.000	1.062	0.087	0.984	0.007	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TNEIVEEQYTPQSL	0.057	0.104	0.059	0.098	1.868	0.901	0.098	1.010	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-4	SCG2
TPLVTLFKNAIIKNAHKKGQ	0.171	0.240	0.200	0.272	2.089	1.063	0.240	0.620	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
VAELDQLLHY	0.731	0.781	0.888	0.898	1.103	0.142	0.781	0.107	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
VANALSHKYH	0.017	0.040	0.036	0.070	2.994	1.582	0.040	1.398	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
VGRPEWWMDYQ	0.332	0.394	0.321	0.403	0.732	-0.450	0.394	0.404	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.001	0.004	0.002	0.006	0.397	-1.335	0.004	2.423	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGF	0.027	0.059	0.046	0.079	1.819	0.863	0.059	1.227	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
Y(+42.01)GGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAH	0.000	0.001	0.000	0.001	0.224	-2.159	0.001	3.141	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNA	0.000	0.000	0.000	0.001	0.071	-3.819	0.000	4.971	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	0.000	0.001	0.000	0.002	0.255	-1.974	0.001	2.848	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.304	0.371	0.200	0.272	0.561	-0.833	0.272	0.566	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YDRVAELDQLLHY	0.230	0.296	0.321	0.403	0.783	-0.353	0.296	0.529	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
YGGFM(+15.99)RF	0.277	0.348	0.481	0.544	1.136	0.184	0.348	0.459	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)RGL	0.681	0.744	0.370	0.446	0.815	-0.295	0.446	0.350	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAHKKGQ	0.946	0.966	0.673	0.727	1.365	0.449	0.727	0.138	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMRF	0.038	0.074	0.021	0.047	1.673	0.743	0.047	1.325	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.011	0.026	0.027	0.060	1.972	0.979	0.026	1.581	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMTSE	0.348	0.403	0.481	0.544	1.249	0.321	0.403	0.394	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNA	0.004	0.013	0.006	0.015	0.490	-1.030	0.013	1.885	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAH	0.008	0.023	0.006	0.015	0.386	-1.374	0.015	1.817	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.034	0.071	0.046	0.079	1.735	0.795	0.071	1.152	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	status	Accession	Name	GN
AGAPEPAEPMELAKPSA	0.001	0.006	0.002	0.006	0.248	-2.011	0.006	2.213	Down	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
EDREEASLQDRQYASHHT	0.007	0.021	0.021	0.047	3.147	1.654	0.021	1.677	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EDREEASLQDRQYASHHTTE	0.001	0.004	0.001	0.003	2.874	1.523	0.003	2.545	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHT	0.000	0.002	0.001	0.003	3.938	1.978	0.002	2.680	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHTTE	0.000	0.003	0.001	0.003	2.415	1.272	0.003	2.545	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPE	0.011	0.027	0.011	0.029	2.349	1.232	0.027	1.563	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQ	0.006	0.018	0.001	0.004	2.518	1.332	0.004	2.355	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.000	0.000	0.000	0.001	4.087	2.031	0.000	4.650	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRDKA	0.000	0.001	0.000	0.001	4.343	2.119	0.001	3.141	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FPTLGGSQDKSLHN	0.000	0.000	0.000	0.001	2.250	1.170	0.000	5.140	Up	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-3	SCG3
GEAYHHVPESQRD	0.001	0.004	0.001	0.004	3.056	1.611	0.004	2.423	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GEAYHHVPESQRDKA	0.001	0.004	0.000	0.001	4.852	2.279	0.001	3.066	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GPEFRDDGAEPGPRE(-.98)	0.002	0.006	0.002	0.009	1.895	0.923	0.006	2.209	Up	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
KVVAGVANALSHKYH	0.006	0.018	0.004	0.012	1.886	0.916	0.012	1.936	Up	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
LAGAPEPA	0.000	0.001	0.000	0.001	0.043	-4.541	0.001	3.141	Down	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
LDQLLHY	0.000	0.000	0.000	0.001	4.580	2.195	0.000	3.902	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LGEAYHHVPESQRD	0.000	0.002	0.000	0.001	5.558	2.475	0.001	3.066	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
MYEENSRDNPF	0.010	0.026	0.021	0.047	1.880	0.911	0.026	1.581	Up	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-3	SCG2
PEFRDDGAEPGPRE(-.98)	0.002	0.009	0.002	0.009	2.148	1.103	0.009	2.066	Up	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Q(-17.03)HWSYGLRPG(-.98)	0.001	0.005	0.006	0.015	2.119	1.084	0.005	2.268	Up	tr|I3MCA0|I3MCA0_ICTTR	Progonadoliberin-1	GNRH1
Q(-17.03)KIAEKFSQ	0.003	0.010	0.001	0.003	3.025	1.597	0.003	2.545	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)KIAEKFSQR(-.98)	0.001	0.004	0.000	0.001	5.746	2.523	0.001	2.890	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPVKVYPNGAEDES(+79.97)AESFPLEF	0.006	0.019	0.000	0.001	0.091	-3.466	0.001	3.066	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RPVKVYPNGAEDESAESFPLEF	0.001	0.006	0.002	0.009	0.232	-2.109	0.006	2.213	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RTLYGFGG	0.003	0.010	0.004	0.012	2.269	1.182	0.010	1.987	Up	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
SANSNPAMAPRE	0.000	0.002	0.001	0.003	3.701	1.888	0.002	2.796	Up	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SLDSPAGPAE	0.003	0.010	0.004	0.012	3.484	1.801	0.010	1.987	Up	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SPQLEDEAKEL	0.007	0.019	0.006	0.015	1.794	0.843	0.015	1.817	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.010	0.026	0.011	0.029	1.542	0.625	0.026	1.581	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SQGGEPGAYLTPDTREE	0.010	0.026	0.002	0.009	1.626	0.701	0.009	2.066	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SVNPYLQGQRL	0.000	0.001	0.001	0.003	6.020	2.590	0.001	3.031	Up	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B2	SCG5
TLGGSQDKSLHN	0.001	0.004	0.000	0.001	4.597	2.201	0.001	3.066	Up	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-4	SCG3
VKMALQQEGFD	0.001	0.004	0.002	0.006	0.397	-1.335	0.004	2.423	Down	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
Y(+42.01)GGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAH	0.000	0.001	0.000	0.001	0.224	-2.159	0.001	3.141	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNA	0.000	0.000	0.000	0.001	0.071	-3.819	0.000	4.971	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	0.000	0.001	0.000	0.002	0.255	-1.974	0.001	2.848	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNA	0.004	0.013	0.006	0.015	0.490	-1.030	0.013	1.885	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAH	0.008	0.023	0.006	0.015	0.386	-1.374	0.015	1.817	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

August vs October

Full stat

Code

contrast = combo_list[[3]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: August over October"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
AADQDLGPEAPPEGVLGA	0.003	0.011	0.003	0.010	0.509	-0.973	0.010	2.002	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.001	0.005	0.000	0.003	0.276	-1.855	0.003	2.510	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AAMDLEL	0.922	0.955	0.605	0.720	0.714	-0.486	0.720	0.143	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AELDQLLHY	0.760	0.851	0.931	0.952	0.929	-0.106	0.851	0.070	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AFGPRGPGLQL	0.728	0.834	0.546	0.675	0.995	-0.008	0.675	0.171	tr|I3MMW2|I3MMW2_ICTTR	Chromogranin-A	CHGA
AGAPEPAEPMELAKPSA	0.000	0.000	0.000	0.001	0.058	-4.119	0.000	4.808	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
ATLESVFQELGKLTGPSSQKRE	0.118	0.217	0.222	0.367	1.410	0.496	0.217	0.663	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-2	SCG2
DDGPYRMEHFRWGSPPKD	0.000	0.000	0.000	0.001	0.232	-2.108	0.000	3.310	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
EDREEASLQDRQYASHHT	0.037	0.084	0.019	0.045	2.058	1.041	0.045	1.345	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EDREEASLQDRQYASHHTTE	0.924	0.955	1.000	1.000	0.945	-0.081	0.955	0.020	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHT	0.001	0.004	0.002	0.008	2.655	1.409	0.004	2.387	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHTTE	0.018	0.046	0.019	0.045	1.475	0.560	0.045	1.345	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EESEESEEGTTSEVT	0.000	0.000	0.000	0.001	4.091	2.032	0.000	3.351	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EIGDEENSAKFPI(-.98)	0.677	0.806	0.796	0.870	0.972	-0.041	0.806	0.094	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
ELDQLLHY	0.020	0.049	0.014	0.036	2.244	1.166	0.036	1.443	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FKNAIIKNAH	0.997	0.997	0.796	0.870	0.638	-0.648	0.870	0.060	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FKNAIIKNAHKKGQ	0.278	0.435	0.136	0.237	0.687	-0.542	0.237	0.626	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FLGEAYHHVPE	0.649	0.783	0.605	0.720	0.833	-0.263	0.720	0.143	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPES	0.283	0.436	0.546	0.675	1.253	0.325	0.436	0.360	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQ	0.057	0.120	0.094	0.177	1.657	0.729	0.120	0.921	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.818	0.894	0.796	0.870	1.113	0.154	0.870	0.060	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRDKA	0.036	0.083	0.050	0.107	2.093	1.066	0.083	1.079	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FPTLGGSQDKSLHN	0.006	0.020	0.008	0.024	1.338	0.420	0.020	1.693	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-3	SCG3
GEAYHHVPESQRD	0.005	0.018	0.006	0.018	2.349	1.232	0.018	1.748	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GEAYHHVPESQRDKA	0.014	0.036	0.006	0.018	2.802	1.486	0.018	1.738	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GGFMRGL	0.299	0.453	0.297	0.458	1.304	0.383	0.453	0.344	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GGPEFRDDGAEPGPRE(-.98)	0.979	0.997	0.863	0.912	0.991	-0.013	0.912	0.040	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GPEFRDDGAEPGPRE(-.98)	0.403	0.557	0.340	0.492	1.126	0.171	0.492	0.308	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GRTLYGFGG	0.148	0.256	0.136	0.237	1.580	0.660	0.237	0.626	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
GVANALSHKYH	0.508	0.663	0.730	0.837	1.519	0.603	0.663	0.179	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
GVLFNPYYDPLQWKSSRFE	0.073	0.141	0.077	0.148	0.449	-1.156	0.141	0.851	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
KVVAGVANALSHKYH	0.526	0.668	0.863	0.912	1.073	0.101	0.668	0.175	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
KYVMGHFRWD	0.001	0.004	0.003	0.010	0.326	-1.616	0.004	2.387	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
KYVMGHFRWDRF(-.98)	0.000	0.000	0.000	0.001	0.199	-2.326	0.000	3.487	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
LAGAPEPA	0.000	0.000	0.000	0.001	0.027	-5.232	0.000	4.808	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
LDQLLHY	0.000	0.004	0.000	0.002	2.323	1.216	0.002	2.714	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LENPQPQAPARRLLPP	0.004	0.016	0.000	0.002	0.494	-1.017	0.002	2.714	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGEAYHHVPESQRD	0.197	0.319	0.258	0.404	1.399	0.484	0.319	0.496	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LGVLFNPYYDPLQWKSSRFE	0.009	0.025	0.008	0.024	0.411	-1.282	0.024	1.628	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
MYEENSRDNPF	0.009	0.025	0.014	0.036	1.725	0.787	0.025	1.599	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-3	SCG2
PEFRDDGAEPGPRE(-.98)	0.347	0.501	0.436	0.603	1.196	0.259	0.501	0.300	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Q(-17.03)EPGAPAAGM	0.576	0.709	0.387	0.550	0.903	-0.147	0.550	0.259	tr|I3MIV6|I3MIV6_ICTTR	Carboxypeptidase E	CPE
Q(-17.03)HWSYGLRPG(-.98)	0.918	0.955	0.730	0.837	1.046	0.065	0.837	0.077	tr|I3MCA0|I3MCA0_ICTTR	Progonadoliberin-1	GNRH1
Q(-17.03)KIAEKFSQ	0.008	0.025	0.003	0.010	2.291	1.196	0.010	2.002	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)KIAEKFSQR(-.98)	0.038	0.084	0.031	0.074	1.801	0.849	0.074	1.131	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)LEDEAKELQ	0.744	0.843	0.730	0.837	1.059	0.083	0.837	0.077	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
Q(-17.03)YDRVAELDQLLHY	0.003	0.011	0.004	0.014	0.277	-1.854	0.011	1.972	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
QYDRVAELDQLLHY	0.065	0.128	0.063	0.128	0.652	-0.617	0.128	0.894	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPVKVYPNGAEDES(+79.97)AESFPLEF	0.000	0.002	0.000	0.001	0.173	-2.531	0.001	3.112	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RPVKVYPNGAEDESAESFPLEF	0.002	0.009	0.000	0.002	0.255	-1.971	0.002	2.714	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RTLYGFGG	0.007	0.022	0.014	0.036	2.079	1.056	0.022	1.668	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
RVLTEEEEKELENL	0.997	0.997	0.931	0.952	1.015	0.022	0.952	0.022	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
S(+42.01)YSMEHFRWGKPV(-.98)	0.000	0.000	0.000	0.001	0.200	-2.324	0.000	3.367	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SANSNPAM(+15.99)APRE	0.001	0.004	0.001	0.005	4.406	2.140	0.004	2.371	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SANSNPAMAPRE	0.006	0.020	0.011	0.030	2.098	1.069	0.020	1.693	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SLDSPAGPA	0.457	0.614	0.340	0.492	1.224	0.291	0.492	0.308	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SLDSPAGPAE	0.077	0.146	0.113	0.209	2.641	1.401	0.146	0.837	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SPQLEDE	0.001	0.006	0.001	0.005	1.989	0.992	0.005	2.278	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKEL	0.305	0.455	0.489	0.630	1.333	0.415	0.455	0.342	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.150	0.256	0.190	0.325	1.254	0.326	0.256	0.592	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SQGGEPGAYLTPDT	0.168	0.282	0.258	0.404	1.294	0.372	0.282	0.550	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQGGEPGAYLTPDTREE	0.180	0.297	0.222	0.367	1.236	0.306	0.297	0.528	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQTPLVTLF	0.489	0.647	0.436	0.603	1.251	0.323	0.603	0.220	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SQTPLVTLFKNAIIKNAHKKGQ	0.395	0.555	0.489	0.630	1.400	0.485	0.555	0.256	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SSQEGNPPSEERGHTLQEPEEAKVGE	0.064	0.127	0.050	0.107	0.679	-0.558	0.107	0.969	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SVNPYLQGQRL	0.064	0.127	0.077	0.148	1.860	0.895	0.127	0.895	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B2	SCG5
SVNPYLQGQRLDNVV	0.013	0.036	0.014	0.036	0.604	-0.729	0.036	1.444	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B3	SCG5
SVNPYLQGQRLDNVVA	0.030	0.071	0.050	0.107	0.703	-0.508	0.071	1.148	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B4	SCG5
SVSTVLTSKYR	0.132	0.237	0.136	0.237	1.545	0.627	0.237	0.626	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SYSMEHF	0.027	0.065	0.050	0.107	1.644	0.717	0.065	1.186	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SYSMEHFRWGKPV(-.98)	0.001	0.004	0.001	0.005	0.315	-1.669	0.004	2.356	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
TLGGSQDKSLHN	0.006	0.020	0.001	0.004	3.125	1.644	0.004	2.389	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-4	SCG3
TLYGFGG	0.773	0.855	0.863	0.912	0.950	-0.074	0.855	0.068	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TNEIVEEQYTPQSL	0.054	0.116	0.063	0.128	1.743	0.801	0.116	0.935	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-4	SCG2
TPLVTLFKNAIIKNAHKKGQ	0.389	0.553	0.796	0.870	1.059	0.083	0.553	0.257	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
VAELDQLLHY	0.860	0.919	1.000	1.000	1.013	0.019	0.919	0.037	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
VANALSHKYH	0.434	0.591	0.340	0.492	1.245	0.316	0.492	0.308	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
VGRPEWWMDYQ	0.710	0.824	0.546	0.675	1.008	0.011	0.675	0.171	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.000	0.000	0.000	0.001	0.298	-1.746	0.000	3.795	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGF	0.581	0.709	0.489	0.630	1.203	0.266	0.630	0.201	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
Y(+42.01)GGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAH	0.000	0.000	0.000	0.001	0.104	-3.269	0.000	4.975	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNA	0.000	0.000	0.000	0.001	0.063	-3.981	0.000	3.795	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	0.000	0.000	0.000	0.001	0.062	-4.002	0.000	4.975	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.001	0.004	0.001	0.005	0.153	-2.706	0.004	2.387	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YDRVAELDQLLHY	0.521	0.668	0.605	0.720	0.923	-0.116	0.668	0.175	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
YGGFM(+15.99)RF	0.014	0.038	0.011	0.030	1.911	0.934	0.030	1.520	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)RGL	0.134	0.237	0.077	0.148	1.133	0.180	0.148	0.831	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAHKKGQ	0.214	0.342	0.258	0.404	1.325	0.406	0.342	0.467	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMRF	0.698	0.820	0.489	0.630	1.073	0.102	0.630	0.201	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.540	0.677	0.489	0.630	0.880	-0.184	0.630	0.201	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMTSE	0.851	0.919	0.931	0.952	0.856	-0.225	0.919	0.037	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNA	0.001	0.004	0.001	0.004	0.429	-1.219	0.004	2.389	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAH	0.001	0.005	0.001	0.004	0.401	-1.317	0.004	2.389	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.342	0.501	0.340	0.492	1.202	0.266	0.492	0.308	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	status	Accession	Name	GN
AADQDLGPEAPPEGVLGA	0.003	0.011	0.003	0.010	0.509	-0.973	0.010	2.002	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.001	0.005	0.000	0.003	0.276	-1.855	0.003	2.510	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AGAPEPAEPMELAKPSA	0.000	0.000	0.000	0.001	0.058	-4.119	0.000	4.808	Down	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
DDGPYRMEHFRWGSPPKD	0.000	0.000	0.000	0.001	0.232	-2.108	0.000	3.310	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
EEASLQDRQYASHHT	0.001	0.004	0.002	0.008	2.655	1.409	0.004	2.387	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHTTE	0.018	0.046	0.019	0.045	1.475	0.560	0.045	1.345	NA	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EESEESEEGTTSEVT	0.000	0.000	0.000	0.001	4.091	2.032	0.000	3.351	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
ELDQLLHY	0.020	0.049	0.014	0.036	2.244	1.166	0.036	1.443	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FPTLGGSQDKSLHN	0.006	0.020	0.008	0.024	1.338	0.420	0.020	1.693	NA	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-3	SCG3
GEAYHHVPESQRD	0.005	0.018	0.006	0.018	2.349	1.232	0.018	1.748	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GEAYHHVPESQRDKA	0.014	0.036	0.006	0.018	2.802	1.486	0.018	1.738	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
KYVMGHFRWD	0.001	0.004	0.003	0.010	0.326	-1.616	0.004	2.387	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
KYVMGHFRWDRF(-.98)	0.000	0.000	0.000	0.001	0.199	-2.326	0.000	3.487	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
LAGAPEPA	0.000	0.000	0.000	0.001	0.027	-5.232	0.000	4.808	Down	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
LDQLLHY	0.000	0.004	0.000	0.002	2.323	1.216	0.002	2.714	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LENPQPQAPARRLLPP	0.004	0.016	0.000	0.002	0.494	-1.017	0.002	2.714	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGVLFNPYYDPLQWKSSRFE	0.009	0.025	0.008	0.024	0.411	-1.282	0.024	1.628	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
MYEENSRDNPF	0.009	0.025	0.014	0.036	1.725	0.787	0.025	1.599	Up	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-3	SCG2
Q(-17.03)KIAEKFSQ	0.008	0.025	0.003	0.010	2.291	1.196	0.010	2.002	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)YDRVAELDQLLHY	0.003	0.011	0.004	0.014	0.277	-1.854	0.011	1.972	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPVKVYPNGAEDES(+79.97)AESFPLEF	0.000	0.002	0.000	0.001	0.173	-2.531	0.001	3.112	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RPVKVYPNGAEDESAESFPLEF	0.002	0.009	0.000	0.002	0.255	-1.971	0.002	2.714	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RTLYGFGG	0.007	0.022	0.014	0.036	2.079	1.056	0.022	1.668	Up	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
S(+42.01)YSMEHFRWGKPV(-.98)	0.000	0.000	0.000	0.001	0.200	-2.324	0.000	3.367	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SANSNPAM(+15.99)APRE	0.001	0.004	0.001	0.005	4.406	2.140	0.004	2.371	Up	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SANSNPAMAPRE	0.006	0.020	0.011	0.030	2.098	1.069	0.020	1.693	Up	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SPQLEDE	0.001	0.006	0.001	0.005	1.989	0.992	0.005	2.278	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SVNPYLQGQRLDNVV	0.013	0.036	0.014	0.036	0.604	-0.729	0.036	1.444	Down	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B3	SCG5
SYSMEHFRWGKPV(-.98)	0.001	0.004	0.001	0.005	0.315	-1.669	0.004	2.356	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
TLGGSQDKSLHN	0.006	0.020	0.001	0.004	3.125	1.644	0.004	2.389	Up	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-4	SCG3
VKMALQQEGFD	0.000	0.000	0.000	0.001	0.298	-1.746	0.000	3.795	Down	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
Y(+42.01)GGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAH	0.000	0.000	0.000	0.001	0.104	-3.269	0.000	4.975	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNA	0.000	0.000	0.000	0.001	0.063	-3.981	0.000	3.795	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	0.000	0.000	0.000	0.001	0.062	-4.002	0.000	4.975	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.001	0.004	0.001	0.005	0.153	-2.706	0.004	2.387	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFM(+15.99)RF	0.014	0.038	0.011	0.030	1.911	0.934	0.030	1.520	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMTSEKSQTPLVTLFKNAIIKNA	0.001	0.004	0.001	0.004	0.429	-1.219	0.004	2.389	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAH	0.001	0.005	0.001	0.004	0.401	-1.317	0.004	2.389	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

August vs Torpor

Full stat

Code

contrast = combo_list[[4]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: August over Torpor"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
AADQDLGPEAPPEGVLGA	0.048	0.099	0.012	0.031	0.444	-1.173	0.031	1.504	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.001	0.005	0.001	0.008	0.116	-3.104	0.005	2.312	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AAMDLEL	0.308	0.438	0.364	0.481	0.304	-1.717	0.438	0.358	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AELDQLLHY	0.992	0.992	0.898	0.918	0.933	-0.099	0.918	0.037	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AFGPRGPGLQL	0.557	0.654	0.797	0.871	0.776	-0.366	0.654	0.184	tr|I3MMW2|I3MMW2_ICTTR	Chromogranin-A	CHGA
AGAPEPAEPMELAKPSA	0.009	0.038	0.001	0.008	0.071	-3.814	0.008	2.106	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
ATLESVFQELGKLTGPSSQKRE	0.841	0.864	0.898	0.918	1.080	0.111	0.864	0.063	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-2	SCG2
DDGPYRMEHFRWGSPPKD	0.006	0.029	0.012	0.031	0.406	-1.300	0.029	1.535	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
EDREEASLQDRQYASHHT	0.016	0.047	0.007	0.023	2.327	1.218	0.023	1.629	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EDREEASLQDRQYASHHTTE	0.070	0.131	0.083	0.153	1.770	0.824	0.131	0.883	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHT	0.001	0.005	0.002	0.013	4.634	2.212	0.005	2.312	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHTTE	0.015	0.047	0.007	0.023	1.898	0.925	0.023	1.629	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EESEESEEGTTSEVT	0.014	0.047	0.012	0.031	4.572	2.193	0.031	1.504	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EIGDEENSAKFPI(-.98)	0.392	0.505	0.298	0.418	0.804	-0.315	0.418	0.379	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
ELDQLLHY	0.074	0.136	0.112	0.195	1.948	0.962	0.136	0.868	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FKNAIIKNAH	0.599	0.695	0.898	0.918	0.883	-0.180	0.695	0.158	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FKNAIIKNAHKKGQ	0.846	0.864	0.364	0.481	0.777	-0.365	0.481	0.317	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FLGEAYHHVPE	0.379	0.502	0.438	0.534	1.251	0.323	0.502	0.299	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPES	0.079	0.142	0.112	0.195	1.741	0.800	0.142	0.847	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQ	0.012	0.044	0.012	0.031	2.223	1.153	0.031	1.504	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.086	0.149	0.083	0.153	1.393	0.478	0.149	0.827	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRDKA	0.031	0.073	0.042	0.088	1.571	0.652	0.073	1.134	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FPTLGGSQDKSLHN	0.983	0.992	0.699	0.783	1.026	0.037	0.783	0.106	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-3	SCG3
GEAYHHVPESQRD	0.004	0.021	0.012	0.031	2.956	1.564	0.021	1.677	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GEAYHHVPESQRDKA	0.014	0.047	0.007	0.023	3.001	1.586	0.023	1.629	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GGFMRGL	0.349	0.468	0.240	0.358	1.779	0.831	0.358	0.446	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GGPEFRDDGAEPGPRE(-.98)	0.018	0.050	0.019	0.045	0.450	-1.153	0.045	1.351	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GPEFRDDGAEPGPRE(-.98)	0.019	0.050	0.007	0.023	0.416	-1.266	0.023	1.629	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GRTLYGFGG	0.654	0.750	0.518	0.617	0.870	-0.200	0.617	0.210	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
GVANALSHKYH	0.459	0.568	0.518	0.617	1.939	0.955	0.568	0.246	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
GVLFNPYYDPLQWKSSRFE	0.055	0.110	0.060	0.117	0.354	-1.497	0.110	0.960	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
KVVAGVANALSHKYH	0.540	0.643	0.298	0.418	0.839	-0.254	0.418	0.379	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
KYVMGHFRWD	0.012	0.044	0.029	0.066	0.439	-1.187	0.044	1.356	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
KYVMGHFRWDRF(-.98)	0.002	0.012	0.007	0.023	0.340	-1.556	0.012	1.905	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
LAGAPEPA	0.000	0.005	0.007	0.023	0.111	-3.170	0.005	2.312	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
LDQLLHY	0.023	0.058	0.012	0.031	2.620	1.390	0.031	1.504	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LENPQPQAPARRLLPP	0.057	0.110	0.019	0.045	0.553	-0.856	0.045	1.351	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGEAYHHVPESQRD	0.044	0.096	0.060	0.117	1.648	0.720	0.096	1.019	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LGVLFNPYYDPLQWKSSRFE	0.000	0.001	0.001	0.008	0.123	-3.020	0.001	3.037	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
MYEENSRDNPF	0.084	0.148	0.147	0.242	1.407	0.493	0.148	0.829	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-3	SCG2
PEFRDDGAEPGPRE(-.98)	0.137	0.229	0.190	0.297	0.583	-0.779	0.229	0.639	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Q(-17.03)EPGAPAAGM	0.002	0.012	0.012	0.031	0.531	-0.914	0.012	1.905	tr|I3MIV6|I3MIV6_ICTTR	Carboxypeptidase E	CPE
Q(-17.03)HWSYGLRPG(-.98)	0.284	0.411	0.298	0.418	0.746	-0.422	0.411	0.386	tr|I3MCA0|I3MCA0_ICTTR	Progonadoliberin-1	GNRH1
Q(-17.03)KIAEKFSQ	0.003	0.017	0.007	0.023	3.432	1.779	0.017	1.761	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)KIAEKFSQR(-.98)	0.008	0.037	0.019	0.045	2.482	1.311	0.037	1.429	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)LEDEAKELQ	0.707	0.801	0.438	0.534	0.813	-0.300	0.534	0.272	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
Q(-17.03)YDRVAELDQLLHY	0.000	0.005	0.001	0.008	0.075	-3.746	0.005	2.312	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
QYDRVAELDQLLHY	0.036	0.081	0.004	0.020	0.320	-1.645	0.020	1.704	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPVKVYPNGAEDES(+79.97)AESFPLEF	0.000	0.005	0.001	0.008	0.106	-3.232	0.005	2.312	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RPVKVYPNGAEDESAESFPLEF	0.049	0.099	0.042	0.088	0.314	-1.673	0.088	1.057	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RTLYGFGG	0.796	0.851	1.000	1.000	0.954	-0.067	0.851	0.070	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
RVLTEEEEKELENL	0.485	0.592	0.898	0.918	1.024	0.034	0.592	0.228	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
S(+42.01)YSMEHFRWGKPV(-.98)	0.000	0.001	0.002	0.013	0.322	-1.634	0.001	3.089	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SANSNPAM(+15.99)APRE	0.742	0.820	1.000	1.000	1.972	0.980	0.820	0.086	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SANSNPAMAPRE	0.018	0.050	0.042	0.088	0.414	-1.271	0.050	1.301	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SLDSPAGPA	0.005	0.024	0.007	0.023	0.299	-1.741	0.023	1.629	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SLDSPAGPAE	0.391	0.505	0.606	0.713	1.688	0.755	0.505	0.297	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SPQLEDE	0.172	0.275	0.083	0.153	0.511	-0.969	0.153	0.816	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKEL	0.026	0.062	0.004	0.020	0.370	-1.435	0.020	1.704	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.833	0.864	0.699	0.783	1.042	0.060	0.783	0.106	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SQGGEPGAYLTPDT	0.034	0.078	0.147	0.242	1.500	0.585	0.078	1.109	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQGGEPGAYLTPDTREE	0.399	0.507	0.438	0.534	1.142	0.191	0.507	0.295	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQTPLVTLF	0.422	0.529	0.438	0.534	0.672	-0.573	0.529	0.277	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SQTPLVTLFKNAIIKNAHKKGQ	0.047	0.099	0.042	0.088	0.301	-1.731	0.088	1.057	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SSQEGNPPSEERGHTLQEPEEAKVGE	0.754	0.824	0.898	0.918	0.918	-0.124	0.824	0.084	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SVNPYLQGQRL	0.002	0.012	0.012	0.031	2.530	1.339	0.012	1.905	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B2	SCG5
SVNPYLQGQRLDNVV	0.012	0.044	0.001	0.008	0.152	-2.721	0.008	2.106	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B3	SCG5
SVNPYLQGQRLDNVVA	0.000	0.005	0.001	0.008	0.342	-1.547	0.005	2.312	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B4	SCG5
SVSTVLTSKYR	0.792	0.851	0.699	0.783	1.009	0.013	0.783	0.106	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SYSMEHF	0.720	0.806	0.898	0.918	0.972	-0.041	0.806	0.094	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SYSMEHFRWGKPV(-.98)	0.150	0.248	0.112	0.195	0.636	-0.653	0.195	0.710	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
TLGGSQDKSLHN	0.013	0.045	0.019	0.045	2.449	1.292	0.045	1.351	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-4	SCG3
TLYGFGG	0.128	0.218	0.147	0.242	0.408	-1.295	0.218	0.661	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TNEIVEEQYTPQSL	0.530	0.638	0.797	0.871	1.162	0.217	0.638	0.195	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-4	SCG2
TPLVTLFKNAIIKNAHKKGQ	0.179	0.276	0.190	0.297	0.380	-1.395	0.276	0.559	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
VAELDQLLHY	0.341	0.468	0.364	0.481	0.764	-0.389	0.468	0.330	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
VANALSHKYH	0.334	0.468	0.438	0.534	1.555	0.637	0.468	0.330	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
VGRPEWWMDYQ	0.022	0.056	0.004	0.020	0.291	-1.779	0.020	1.704	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.001	0.005	0.001	0.008	0.345	-1.533	0.005	2.312	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGF	0.157	0.255	0.438	0.534	0.597	-0.743	0.255	0.594	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
Y(+42.01)GGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAH	0.010	0.039	0.004	0.020	0.248	-2.009	0.020	1.704	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNA	0.001	0.010	0.001	0.008	0.076	-3.710	0.008	2.106	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	0.000	0.000	0.001	0.008	0.105	-3.258	0.000	4.077	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.276	0.406	0.298	0.418	0.523	-0.935	0.406	0.392	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YDRVAELDQLLHY	0.000	0.005	0.001	0.008	0.252	-1.987	0.005	2.312	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
YGGFM(+15.99)RF	0.824	0.864	0.699	0.783	0.912	-0.133	0.783	0.106	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)RGL	0.346	0.468	0.364	0.481	0.564	-0.826	0.468	0.330	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAHKKGQ	0.268	0.399	0.240	0.358	0.723	-0.468	0.358	0.446	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMRF	0.019	0.050	0.002	0.013	0.479	-1.063	0.013	1.902	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.017	0.048	0.007	0.023	0.397	-1.334	0.023	1.629	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMTSE	0.213	0.322	0.240	0.358	0.611	-0.711	0.322	0.492	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNA	0.002	0.013	0.001	0.008	0.204	-2.290	0.008	2.106	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAH	0.057	0.110	0.060	0.117	0.519	-0.946	0.110	0.958	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.178	0.276	0.190	0.297	1.349	0.432	0.276	0.559	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	status	Accession	Name	GN
AADQDLGPEAPPEGVLGAL	0.001	0.005	0.001	0.008	0.116	-3.104	0.005	2.312	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AGAPEPAEPMELAKPSA	0.009	0.038	0.001	0.008	0.071	-3.814	0.008	2.106	Down	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
DDGPYRMEHFRWGSPPKD	0.006	0.029	0.012	0.031	0.406	-1.300	0.029	1.535	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
EDREEASLQDRQYASHHT	0.016	0.047	0.007	0.023	2.327	1.218	0.023	1.629	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHT	0.001	0.005	0.002	0.013	4.634	2.212	0.005	2.312	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHTTE	0.015	0.047	0.007	0.023	1.898	0.925	0.023	1.629	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EESEESEEGTTSEVT	0.014	0.047	0.012	0.031	4.572	2.193	0.031	1.504	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQ	0.012	0.044	0.012	0.031	2.223	1.153	0.031	1.504	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GEAYHHVPESQRD	0.004	0.021	0.012	0.031	2.956	1.564	0.021	1.677	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GEAYHHVPESQRDKA	0.014	0.047	0.007	0.023	3.001	1.586	0.023	1.629	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
KYVMGHFRWDRF(-.98)	0.002	0.012	0.007	0.023	0.340	-1.556	0.012	1.905	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
LAGAPEPA	0.000	0.005	0.007	0.023	0.111	-3.170	0.005	2.312	Down	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
LGVLFNPYYDPLQWKSSRFE	0.000	0.001	0.001	0.008	0.123	-3.020	0.001	3.037	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)EPGAPAAGM	0.002	0.012	0.012	0.031	0.531	-0.914	0.012	1.905	Down	tr|I3MIV6|I3MIV6_ICTTR	Carboxypeptidase E	CPE
Q(-17.03)KIAEKFSQ	0.003	0.017	0.007	0.023	3.432	1.779	0.017	1.761	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)KIAEKFSQR(-.98)	0.008	0.037	0.019	0.045	2.482	1.311	0.037	1.429	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)YDRVAELDQLLHY	0.000	0.005	0.001	0.008	0.075	-3.746	0.005	2.312	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPVKVYPNGAEDES(+79.97)AESFPLEF	0.000	0.005	0.001	0.008	0.106	-3.232	0.005	2.312	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
S(+42.01)YSMEHFRWGKPV(-.98)	0.000	0.001	0.002	0.013	0.322	-1.634	0.001	3.089	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SLDSPAGPA	0.005	0.024	0.007	0.023	0.299	-1.741	0.023	1.629	Down	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SVNPYLQGQRL	0.002	0.012	0.012	0.031	2.530	1.339	0.012	1.905	Up	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B2	SCG5
SVNPYLQGQRLDNVV	0.012	0.044	0.001	0.008	0.152	-2.721	0.008	2.106	Down	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B3	SCG5
SVNPYLQGQRLDNVVA	0.000	0.005	0.001	0.008	0.342	-1.547	0.005	2.312	Down	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B4	SCG5
TLGGSQDKSLHN	0.013	0.045	0.019	0.045	2.449	1.292	0.045	1.351	Up	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-4	SCG3
VKMALQQEGFD	0.001	0.005	0.001	0.008	0.345	-1.533	0.005	2.312	Down	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
Y(+42.01)GGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAH	0.010	0.039	0.004	0.020	0.248	-2.009	0.020	1.704	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNA	0.001	0.010	0.001	0.008	0.076	-3.710	0.008	2.106	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	0.000	0.000	0.001	0.008	0.105	-3.258	0.000	4.077	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YDRVAELDQLLHY	0.000	0.005	0.001	0.008	0.252	-1.987	0.005	2.312	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
YGGFMRGL	0.017	0.048	0.007	0.023	0.397	-1.334	0.023	1.629	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMTSEKSQTPLVTLFKNAIIKNA	0.002	0.013	0.001	0.008	0.204	-2.290	0.008	2.106	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

IBA vs March

Full stat

Code

contrast = combo_list[[5]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: IBA over March"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
AADQDLGPEAPPEGVLGA	0.173	0.363	0.020	0.078	1.397	0.483	0.078	1.106	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.003	0.032	0.008	0.042	4.052	2.018	0.032	1.491	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AAMDLEL	0.181	0.363	0.181	0.362	1.452	0.538	0.362	0.441	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AELDQLLHY	0.051	0.154	0.043	0.129	2.413	1.271	0.129	0.889	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AFGPRGPGLQL	0.008	0.049	0.008	0.042	2.314	1.210	0.042	1.379	tr|I3MMW2|I3MMW2_ICTTR	Chromogranin-A	CHGA
AGAPEPAEPMELAKPSA	0.529	0.638	0.573	0.708	0.921	-0.118	0.638	0.195	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
ATLESVFQELGKLTGPSSQKRE	0.416	0.575	0.573	0.708	1.051	0.072	0.575	0.240	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-2	SCG2
DDGPYRMEHFRWGSPPKD	0.522	0.638	0.414	0.572	1.376	0.460	0.572	0.243	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
EDREEASLQDRQYASHHT	0.520	0.638	0.282	0.450	1.388	0.473	0.450	0.347	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EDREEASLQDRQYASHHTTE	0.192	0.368	0.228	0.398	1.485	0.571	0.368	0.434	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHT	0.337	0.561	0.282	0.450	0.866	-0.208	0.450	0.347	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHTTE	0.527	0.638	0.755	0.844	1.182	0.241	0.638	0.195	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EESEESEEGTTSEVT	0.053	0.155	0.108	0.241	0.505	-0.986	0.155	0.809	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EIGDEENSAKFPI(-.98)	0.726	0.802	0.662	0.768	1.177	0.235	0.768	0.114	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
ELDQLLHY	0.392	0.575	0.059	0.159	1.518	0.602	0.159	0.798	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FKNAIIKNAH	0.965	0.976	0.950	0.970	1.007	0.010	0.970	0.013	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FKNAIIKNAHKKGQ	0.175	0.363	0.282	0.450	0.637	-0.651	0.363	0.441	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FLGEAYHHVPE	0.477	0.638	0.414	0.572	1.283	0.359	0.572	0.243	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPES	0.913	0.948	0.950	0.970	1.022	0.031	0.948	0.023	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQ	0.141	0.323	0.228	0.398	1.423	0.509	0.323	0.491	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.000	0.003	0.001	0.010	2.671	1.418	0.003	2.549	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRDKA	0.034	0.125	0.059	0.159	1.794	0.843	0.125	0.904	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FPTLGGSQDKSLHN	0.000	0.004	0.001	0.010	1.761	0.816	0.004	2.424	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-3	SCG3
GEAYHHVPESQRD	0.292	0.508	0.228	0.398	0.879	-0.186	0.398	0.400	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GEAYHHVPESQRDKA	0.357	0.569	0.414	0.572	1.216	0.282	0.569	0.245	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GGFMRGL	0.485	0.638	0.573	0.708	1.277	0.353	0.638	0.195	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GGPEFRDDGAEPGPRE(-.98)	0.000	0.005	0.005	0.034	3.568	1.835	0.005	2.326	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GPEFRDDGAEPGPRE(-.98)	0.000	0.000	0.001	0.010	3.690	1.884	0.000	3.454	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GRTLYGFGG	0.008	0.049	0.013	0.059	2.724	1.446	0.049	1.311	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
GVANALSHKYH	0.049	0.152	0.043	0.129	4.616	2.207	0.129	0.889	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
GVLFNPYYDPLQWKSSRFE	0.064	0.172	0.081	0.201	2.037	1.027	0.172	0.764	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
KVVAGVANALSHKYH	0.057	0.157	0.043	0.129	1.811	0.857	0.129	0.889	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
KYVMGHFRWD	0.479	0.638	0.950	0.970	0.930	-0.105	0.638	0.195	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
KYVMGHFRWDRF(-.98)	0.109	0.269	0.108	0.241	1.645	0.718	0.241	0.617	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
LAGAPEPA	0.045	0.144	0.043	0.129	0.183	-2.451	0.129	0.889	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
LDQLLHY	0.006	0.043	0.008	0.042	1.949	0.963	0.042	1.379	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LENPQPQAPARRLLPP	0.013	0.063	0.020	0.078	1.827	0.869	0.063	1.201	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGEAYHHVPESQRD	0.001	0.017	0.001	0.010	2.891	1.532	0.010	1.982	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LGVLFNPYYDPLQWKSSRFE	0.036	0.125	0.043	0.129	3.434	1.780	0.125	0.904	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
MYEENSRDNPF	0.591	0.686	0.755	0.844	1.172	0.228	0.686	0.163	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-3	SCG2
PEFRDDGAEPGPRE(-.98)	0.010	0.051	0.008	0.042	2.297	1.200	0.042	1.379	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Q(-17.03)EPGAPAAGM	0.997	0.997	0.282	0.450	1.090	0.124	0.450	0.347	tr|I3MIV6|I3MIV6_ICTTR	Carboxypeptidase E	CPE
Q(-17.03)HWSYGLRPG(-.98)	0.005	0.039	0.001	0.010	4.553	2.187	0.010	1.982	tr|I3MCA0|I3MCA0_ICTTR	Progonadoliberin-1	GNRH1
Q(-17.03)KIAEKFSQ	0.354	0.569	0.345	0.515	1.186	0.246	0.515	0.288	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)KIAEKFSQR(-.98)	0.115	0.278	0.108	0.241	1.504	0.589	0.241	0.617	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)LEDEAKELQ	0.243	0.440	0.059	0.159	1.554	0.636	0.159	0.798	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
Q(-17.03)YDRVAELDQLLHY	0.000	0.004	0.001	0.014	6.294	2.654	0.004	2.424	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
QYDRVAELDQLLHY	0.700	0.793	0.662	0.768	1.334	0.416	0.768	0.114	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPVKVYPNGAEDES(+79.97)AESFPLEF	0.403	0.575	0.852	0.920	0.915	-0.129	0.575	0.240	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RPVKVYPNGAEDESAESFPLEF	0.210	0.395	0.345	0.515	1.615	0.692	0.395	0.404	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RTLYGFGG	0.009	0.050	0.005	0.034	2.616	1.388	0.034	1.472	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
RVLTEEEEKELENL	0.340	0.561	1.000	1.000	0.909	-0.138	0.561	0.251	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
S(+42.01)YSMEHFRWGKPV(-.98)	0.178	0.363	0.228	0.398	1.301	0.380	0.363	0.441	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SANSNPAM(+15.99)APRE	0.388	0.575	0.573	0.708	0.834	-0.262	0.575	0.240	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SANSNPAMAPRE	0.006	0.043	0.003	0.023	3.354	1.746	0.023	1.643	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SLDSPAGPA	0.918	0.948	0.573	0.708	1.262	0.336	0.708	0.150	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SLDSPAGPAE	0.407	0.575	0.345	0.515	1.023	0.032	0.515	0.288	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SPQLEDE	0.931	0.951	0.662	0.768	1.542	0.624	0.768	0.114	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKEL	0.021	0.095	0.001	0.014	2.672	1.418	0.014	1.857	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.734	0.802	0.414	0.572	0.964	-0.053	0.572	0.243	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SQGGEPGAYLTPDT	0.509	0.638	0.345	0.515	1.275	0.350	0.515	0.288	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQGGEPGAYLTPDTREE	0.024	0.103	0.013	0.059	1.541	0.623	0.059	1.226	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQTPLVTLF	0.399	0.575	0.852	0.920	1.262	0.336	0.575	0.240	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SQTPLVTLFKNAIIKNAHKKGQ	0.126	0.295	0.108	0.241	3.770	1.915	0.241	0.617	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SSQEGNPPSEERGHTLQEPEEAKVGE	0.397	0.575	0.491	0.650	1.203	0.266	0.575	0.240	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SVNPYLQGQRL	0.006	0.043	0.008	0.042	2.797	1.484	0.042	1.379	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B2	SCG5
SVNPYLQGQRLDNVV	0.092	0.233	0.181	0.362	2.111	1.078	0.233	0.633	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B3	SCG5
SVNPYLQGQRLDNVVA	0.001	0.014	0.001	0.010	2.900	1.536	0.010	1.982	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B4	SCG5
SVSTVLTSKYR	0.285	0.506	0.228	0.398	1.568	0.649	0.398	0.400	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SYSMEHF	0.298	0.510	0.181	0.362	1.212	0.278	0.362	0.441	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SYSMEHFRWGKPV(-.98)	0.056	0.157	0.081	0.201	1.920	0.941	0.157	0.803	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
TLGGSQDKSLHN	0.068	0.177	0.020	0.078	1.863	0.897	0.078	1.106	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-4	SCG3
TLYGFGG	0.574	0.674	0.950	0.970	1.553	0.635	0.674	0.171	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TNEIVEEQYTPQSL	0.859	0.907	0.852	0.920	1.128	0.174	0.907	0.042	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-4	SCG2
TPLVTLFKNAIIKNAHKKGQ	0.162	0.355	0.142	0.303	2.404	1.266	0.303	0.518	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
VAELDQLLHY	0.402	0.575	0.228	0.398	1.741	0.800	0.398	0.400	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
VANALSHKYH	0.029	0.113	0.059	0.159	2.973	1.572	0.113	0.948	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
VGRPEWWMDYQ	0.549	0.653	0.491	0.650	1.096	0.132	0.650	0.187	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.720	0.802	0.662	0.768	1.123	0.167	0.768	0.114	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGF	0.029	0.113	0.043	0.129	2.250	1.170	0.113	0.948	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
Y(+42.01)GGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAH	0.493	0.638	0.755	0.844	1.315	0.395	0.638	0.195	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNA	0.145	0.325	0.228	0.398	0.655	-0.611	0.325	0.488	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	0.412	0.575	0.491	0.650	1.216	0.282	0.575	0.240	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.621	0.712	0.662	0.768	0.907	-0.141	0.712	0.148	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YDRVAELDQLLHY	0.039	0.131	0.029	0.110	2.331	1.221	0.110	0.958	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
YGGFM(+15.99)RF	0.785	0.848	0.950	0.970	0.688	-0.539	0.848	0.072	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)RGL	0.524	0.638	1.000	1.000	0.770	-0.376	0.638	0.195	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAHKKGQ	0.827	0.883	0.414	0.572	1.567	0.648	0.572	0.243	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMRF	0.004	0.039	0.003	0.023	2.943	1.557	0.023	1.643	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.004	0.039	0.001	0.014	2.924	1.548	0.014	1.857	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMTSE	0.188	0.368	0.142	0.303	1.518	0.602	0.303	0.518	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNA	0.217	0.400	0.282	0.450	1.397	0.482	0.400	0.398	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAH	0.036	0.125	0.081	0.201	0.561	-0.835	0.125	0.904	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.015	0.073	0.020	0.078	1.951	0.964	0.073	1.138	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	status	Accession	Name	GN
AADQDLGPEAPPEGVLGAL	0.003	0.032	0.008	0.042	4.052	2.018	0.032	1.491	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AFGPRGPGLQL	0.008	0.049	0.008	0.042	2.314	1.210	0.042	1.379	Up	tr|I3MMW2|I3MMW2_ICTTR	Chromogranin-A	CHGA
FLGEAYHHVPESQRD	0.000	0.003	0.001	0.010	2.671	1.418	0.003	2.549	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FPTLGGSQDKSLHN	0.000	0.004	0.001	0.010	1.761	0.816	0.004	2.424	Up	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-3	SCG3
GGPEFRDDGAEPGPRE(-.98)	0.000	0.005	0.005	0.034	3.568	1.835	0.005	2.326	Up	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GPEFRDDGAEPGPRE(-.98)	0.000	0.000	0.001	0.010	3.690	1.884	0.000	3.454	Up	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
LDQLLHY	0.006	0.043	0.008	0.042	1.949	0.963	0.042	1.379	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LGEAYHHVPESQRD	0.001	0.017	0.001	0.010	2.891	1.532	0.010	1.982	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)HWSYGLRPG(-.98)	0.005	0.039	0.001	0.010	4.553	2.187	0.010	1.982	Up	tr|I3MCA0|I3MCA0_ICTTR	Progonadoliberin-1	GNRH1
Q(-17.03)YDRVAELDQLLHY	0.000	0.004	0.001	0.014	6.294	2.654	0.004	2.424	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RTLYGFGG	0.009	0.050	0.005	0.034	2.616	1.388	0.034	1.472	Up	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
SANSNPAMAPRE	0.006	0.043	0.003	0.023	3.354	1.746	0.023	1.643	Up	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SVNPYLQGQRL	0.006	0.043	0.008	0.042	2.797	1.484	0.042	1.379	Up	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B2	SCG5
SVNPYLQGQRLDNVVA	0.001	0.014	0.001	0.010	2.900	1.536	0.010	1.982	Up	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B4	SCG5
YGGFMRF	0.004	0.039	0.003	0.023	2.943	1.557	0.023	1.643	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.004	0.039	0.001	0.014	2.924	1.548	0.014	1.857	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

IBA vs October

Full stat

Code

contrast = combo_list[[6]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: IBA over October"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
AADQDLGPEAPPEGVLGA	0.779	0.833	0.689	0.809	1.057	0.080	0.809	0.092	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.106	0.276	0.088	0.217	2.324	1.216	0.217	0.663	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AAMDLEL	0.565	0.717	0.607	0.761	1.661	0.732	0.717	0.144	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AELDQLLHY	0.269	0.490	0.272	0.465	1.462	0.548	0.465	0.332	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AFGPRGPGLQL	0.525	0.676	0.036	0.125	1.633	0.708	0.125	0.902	tr|I3MMW2|I3MMW2_ICTTR	Chromogranin-A	CHGA
AGAPEPAEPMELAKPSA	0.003	0.037	0.005	0.056	0.214	-2.226	0.037	1.435	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
ATLESVFQELGKLTGPSSQKRE	0.339	0.549	0.224	0.421	1.191	0.252	0.421	0.376	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-2	SCG2
DDGPYRMEHFRWGSPPKD	0.000	0.011	0.000	0.019	0.425	-1.236	0.011	1.949	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
EDREEASLQDRQYASHHT	0.510	0.676	0.689	0.809	0.908	-0.139	0.676	0.170	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EDREEASLQDRQYASHHTTE	0.006	0.049	0.003	0.044	0.489	-1.034	0.044	1.358	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHT	0.009	0.068	0.008	0.071	0.583	-0.777	0.068	1.169	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHTTE	0.022	0.115	0.036	0.125	0.722	-0.470	0.115	0.940	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EESEESEEGTTSEVT	0.592	0.732	0.607	0.761	1.128	0.173	0.732	0.135	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EIGDEENSAKFPI(-.98)	0.512	0.676	0.689	0.809	1.216	0.282	0.676	0.170	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
ELDQLLHY	0.110	0.277	0.088	0.217	1.740	0.799	0.217	0.663	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FKNAIIKNAH	0.177	0.386	0.181	0.362	0.576	-0.797	0.362	0.441	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FKNAIIKNAHKKGQ	0.363	0.563	0.388	0.589	0.869	-0.202	0.563	0.249	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FLGEAYHHVPE	0.027	0.123	0.026	0.105	0.455	-1.135	0.105	0.981	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPES	0.413	0.588	0.529	0.720	0.827	-0.274	0.588	0.231	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQ	0.852	0.890	0.776	0.848	0.936	-0.095	0.848	0.072	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.043	0.148	0.145	0.316	0.727	-0.459	0.148	0.829	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRDKA	0.339	0.549	0.456	0.670	0.864	-0.210	0.549	0.260	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FPTLGGSQDKSLHN	0.693	0.794	0.864	0.902	1.047	0.066	0.794	0.100	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-3	SCG3
GEAYHHVPESQRD	0.024	0.118	0.050	0.146	0.676	-0.566	0.118	0.930	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GEAYHHVPESQRDKA	0.337	0.549	0.272	0.465	0.702	-0.510	0.465	0.332	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GGFMRGL	0.711	0.804	0.607	0.761	1.117	0.160	0.761	0.119	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GGPEFRDDGAEPGPRE(-.98)	0.002	0.033	0.005	0.056	2.270	1.183	0.033	1.479	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GPEFRDDGAEPGPRE(-.98)	0.000	0.011	0.003	0.044	2.192	1.132	0.011	1.949	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GRTLYGFGG	0.027	0.123	0.036	0.125	2.259	1.176	0.123	0.911	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
GVANALSHKYH	0.281	0.498	0.529	0.720	1.808	0.854	0.498	0.302	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
GVLFNPYYDPLQWKSSRFE	0.984	0.984	0.776	0.848	1.090	0.124	0.848	0.072	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
KVVAGVANALSHKYH	0.600	0.732	0.864	0.902	1.030	0.042	0.732	0.135	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
KYVMGHFRWD	0.006	0.049	0.026	0.105	0.524	-0.934	0.049	1.310	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
KYVMGHFRWDRF(-.98)	0.005	0.049	0.018	0.092	0.413	-1.276	0.049	1.310	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
LAGAPEPA	0.029	0.123	0.050	0.146	0.113	-3.142	0.123	0.911	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
LDQLLHY	0.747	0.807	0.607	0.761	0.989	-0.016	0.761	0.119	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LENPQPQAPARRLLPP	0.727	0.804	0.689	0.809	1.006	0.008	0.804	0.095	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGEAYHHVPESQRD	0.194	0.414	0.181	0.362	0.728	-0.459	0.362	0.441	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LGVLFNPYYDPLQWKSSRFE	0.033	0.129	0.050	0.146	2.637	1.399	0.129	0.890	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
MYEENSRDNPF	0.747	0.807	0.955	0.965	1.075	0.104	0.807	0.093	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-3	SCG2
PEFRDDGAEPGPRE(-.98)	0.271	0.490	0.328	0.540	1.280	0.356	0.490	0.310	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Q(-17.03)EPGAPAAGM	0.256	0.490	0.224	0.421	1.225	0.293	0.421	0.376	tr|I3MIV6|I3MIV6_ICTTR	Carboxypeptidase E	CPE
Q(-17.03)HWSYGLRPG(-.98)	0.052	0.174	0.018	0.092	2.247	1.168	0.092	1.037	tr|I3MCA0|I3MCA0_ICTTR	Progonadoliberin-1	GNRH1
Q(-17.03)KIAEKFSQ	0.722	0.804	0.955	0.965	0.898	-0.155	0.804	0.095	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)KIAEKFSQR(-.98)	0.112	0.277	0.113	0.260	0.471	-1.085	0.260	0.585	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)LEDEAKELQ	0.608	0.732	0.776	0.848	0.856	-0.224	0.732	0.135	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
Q(-17.03)YDRVAELDQLLHY	0.003	0.037	0.002	0.038	4.163	2.058	0.037	1.435	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
QYDRVAELDQLLHY	0.587	0.732	0.776	0.848	1.265	0.339	0.732	0.135	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPVKVYPNGAEDES(+79.97)AESFPLEF	0.035	0.130	0.036	0.125	1.748	0.806	0.125	0.902	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RPVKVYPNGAEDESAESFPLEF	0.057	0.179	0.026	0.105	1.778	0.830	0.105	0.981	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RTLYGFGG	0.015	0.086	0.018	0.092	2.398	1.262	0.086	1.064	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
RVLTEEEEKELENL	0.376	0.564	0.224	0.421	0.989	-0.017	0.421	0.376	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
S(+42.01)YSMEHFRWGKPV(-.98)	0.004	0.045	0.008	0.071	0.411	-1.283	0.045	1.344	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SANSNPAM(+15.99)APRE	0.680	0.789	0.776	0.848	1.099	0.137	0.789	0.103	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SANSNPAMAPRE	0.062	0.189	0.018	0.092	1.902	0.927	0.092	1.037	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SLDSPAGPA	0.405	0.585	0.456	0.670	1.471	0.556	0.585	0.233	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SLDSPAGPAE	0.968	0.978	0.864	0.902	0.775	-0.367	0.902	0.045	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SPQLEDE	0.954	0.975	0.864	0.902	0.791	-0.337	0.902	0.045	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKEL	0.082	0.221	0.026	0.105	1.986	0.990	0.105	0.981	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.518	0.676	0.529	0.720	0.784	-0.352	0.676	0.170	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SQGGEPGAYLTPDT	0.673	0.789	0.776	0.848	0.940	-0.090	0.789	0.103	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQGGEPGAYLTPDTREE	0.348	0.554	0.181	0.362	1.172	0.228	0.362	0.441	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQTPLVTLF	0.122	0.291	0.066	0.189	2.170	1.118	0.189	0.724	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SQTPLVTLFKNAIIKNAHKKGQ	0.309	0.528	0.328	0.540	1.641	0.715	0.528	0.277	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SSQEGNPPSEERGHTLQEPEEAKVGE	0.071	0.208	0.050	0.146	0.580	-0.786	0.146	0.837	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SVNPYLQGQRL	0.270	0.490	0.388	0.589	0.864	-0.211	0.490	0.310	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B2	SCG5
SVNPYLQGQRLDNVV	0.036	0.130	0.088	0.217	2.150	1.104	0.130	0.888	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B3	SCG5
SVNPYLQGQRLDNVVA	0.020	0.110	0.026	0.105	1.919	0.940	0.105	0.981	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B4	SCG5
SVSTVLTSKYR	0.434	0.609	0.607	0.761	1.325	0.406	0.609	0.215	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SYSMEHF	0.239	0.490	0.181	0.362	1.263	0.337	0.362	0.441	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SYSMEHFRWGKPV(-.98)	0.005	0.049	0.012	0.092	0.409	-1.290	0.049	1.310	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
TLGGSQDKSLHN	0.366	0.563	0.689	0.809	1.267	0.341	0.563	0.249	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-4	SCG3
TLYGFGG	0.308	0.528	0.272	0.465	1.389	0.474	0.465	0.332	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TNEIVEEQYTPQSL	0.909	0.939	1.000	1.000	1.052	0.074	0.939	0.027	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-4	SCG2
TPLVTLFKNAIIKNAHKKGQ	0.378	0.564	0.388	0.589	1.219	0.286	0.564	0.249	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
VAELDQLLHY	0.054	0.177	0.113	0.260	1.599	0.677	0.177	0.753	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
VANALSHKYH	0.656	0.781	0.529	0.720	1.236	0.306	0.720	0.143	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
VGRPEWWMDYQ	0.124	0.291	0.050	0.146	1.508	0.593	0.146	0.837	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.398	0.585	0.388	0.589	0.844	-0.245	0.585	0.233	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGF	0.252	0.490	0.388	0.589	1.488	0.573	0.490	0.310	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
Y(+42.01)GGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAH	0.074	0.210	0.272	0.465	0.609	-0.716	0.210	0.678	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNA	0.076	0.210	0.088	0.217	0.585	-0.773	0.210	0.678	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	0.001	0.031	0.002	0.038	0.298	-1.747	0.031	1.512	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.000	0.011	0.000	0.019	0.248	-2.014	0.011	1.949	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YDRVAELDQLLHY	0.015	0.086	0.012	0.092	2.747	1.458	0.086	1.064	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
YGGFM(+15.99)RF	0.269	0.490	0.088	0.217	1.158	0.211	0.217	0.663	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)RGL	0.461	0.628	0.145	0.316	1.071	0.099	0.316	0.500	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAHKKGQ	0.144	0.323	0.113	0.260	1.521	0.605	0.260	0.585	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMRF	0.030	0.123	0.018	0.092	1.888	0.917	0.092	1.037	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.270	0.490	0.272	0.465	1.305	0.384	0.465	0.332	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMTSE	0.796	0.841	0.955	0.965	1.040	0.057	0.841	0.075	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNA	0.448	0.620	0.529	0.720	1.225	0.293	0.620	0.208	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAH	0.014	0.086	0.018	0.092	0.583	-0.778	0.086	1.064	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.141	0.323	0.607	0.761	1.352	0.435	0.323	0.490	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	status	Accession	Name	GN
DDGPYRMEHFRWGSPPKD	0.000	0.011	0.000	0.019	0.425	-1.236	0.011	1.949	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
EDREEASLQDRQYASHHTTE	0.006	0.049	0.003	0.044	0.489	-1.034	0.044	1.358	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GPEFRDDGAEPGPRE(-.98)	0.000	0.011	0.003	0.044	2.192	1.132	0.011	1.949	Up	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Q(-17.03)YDRVAELDQLLHY	0.003	0.037	0.002	0.038	4.163	2.058	0.037	1.435	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	0.001	0.031	0.002	0.038	0.298	-1.747	0.031	1.512	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.000	0.011	0.000	0.019	0.248	-2.014	0.011	1.949	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

IBA vs Torpor

Full stat

Code

contrast = combo_list[[7]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: IBA over Torpor"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
AADQDLGPEAPPEGVLGA	0.549	0.860	0.931	0.972	0.920	-0.120	0.860	0.066	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.808	0.938	0.662	0.916	0.978	-0.033	0.916	0.038	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AAMDLEL	0.475	0.830	0.931	0.972	0.708	-0.499	0.830	0.081	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AELDQLLHY	0.632	0.882	0.662	0.916	1.469	0.555	0.882	0.055	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AFGPRGPGLQL	0.233	0.751	0.537	0.901	1.274	0.350	0.751	0.125	tr|I3MMW2|I3MMW2_ICTTR	Chromogranin-A	CHGA
AGAPEPAEPMELAKPSA	0.052	0.751	0.030	0.570	0.264	-1.921	0.570	0.244	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
ATLESVFQELGKLTGPSSQKRE	0.931	0.974	0.931	0.972	0.912	-0.133	0.972	0.012	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-2	SCG2
DDGPYRMEHFRWGSPPKD	0.072	0.751	0.052	0.787	0.743	-0.428	0.751	0.125	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
EDREEASLQDRQYASHHT	0.995	0.995	0.931	0.972	1.027	0.038	0.972	0.012	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EDREEASLQDRQYASHHTTE	0.656	0.882	0.931	0.972	0.915	-0.128	0.882	0.055	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHT	0.801	0.938	0.329	0.790	1.018	0.026	0.790	0.102	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHTTE	0.571	0.865	0.329	0.790	0.929	-0.106	0.790	0.102	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EESEESEEGTTSEVT	0.774	0.921	0.792	0.955	1.260	0.334	0.921	0.036	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EIGDEENSAKFPI(-.98)	0.916	0.974	1.000	1.000	1.006	0.008	0.974	0.012	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
ELDQLLHY	0.340	0.751	0.792	0.955	1.511	0.595	0.751	0.125	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FKNAIIKNAH	0.651	0.882	0.931	0.972	0.797	-0.328	0.882	0.055	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FKNAIIKNAHKKGQ	0.927	0.974	1.000	1.000	0.983	-0.024	0.974	0.012	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FLGEAYHHVPE	0.300	0.751	0.247	0.790	0.683	-0.549	0.751	0.125	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPES	0.689	0.899	0.429	0.790	1.149	0.200	0.790	0.102	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQ	0.315	0.751	0.429	0.790	1.256	0.329	0.751	0.125	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.479	0.830	0.792	0.955	0.911	-0.135	0.830	0.081	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRDKA	0.071	0.751	0.247	0.790	0.649	-0.624	0.751	0.125	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FPTLGGSQDKSLHN	0.203	0.751	0.177	0.790	0.803	-0.317	0.751	0.125	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-3	SCG3
GEAYHHVPESQRD	0.321	0.751	0.126	0.787	0.850	-0.234	0.751	0.125	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GEAYHHVPESQRDKA	0.534	0.851	0.662	0.916	0.752	-0.411	0.851	0.070	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GGFMRGL	0.598	0.882	0.429	0.790	1.524	0.608	0.790	0.102	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GGPEFRDDGAEPGPRE(-.98)	0.913	0.974	0.931	0.972	1.030	0.042	0.972	0.012	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GPEFRDDGAEPGPRE(-.98)	0.340	0.751	0.429	0.790	0.810	-0.305	0.751	0.125	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GRTLYGFGG	0.427	0.830	0.429	0.790	1.245	0.316	0.790	0.102	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
GVANALSHKYH	0.257	0.751	0.429	0.790	2.307	1.206	0.751	0.125	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
GVLFNPYYDPLQWKSSRFE	0.369	0.775	0.247	0.790	0.861	-0.217	0.775	0.111	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
KVVAGVANALSHKYH	0.751	0.905	0.429	0.790	0.805	-0.313	0.790	0.102	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
KYVMGHFRWD	0.112	0.751	0.126	0.787	0.705	-0.505	0.751	0.125	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
KYVMGHFRWDRF(-.98)	0.248	0.751	0.329	0.790	0.705	-0.505	0.751	0.125	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
LAGAPEPA	0.746	0.905	0.662	0.916	0.473	-1.080	0.905	0.043	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
LDQLLHY	0.957	0.978	0.931	0.972	1.115	0.157	0.972	0.012	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LENPQPQAPARRLLPP	0.926	0.974	0.931	0.972	1.124	0.169	0.972	0.012	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGEAYHHVPESQRD	0.699	0.899	0.329	0.790	0.857	-0.223	0.790	0.102	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LGVLFNPYYDPLQWKSSRFE	0.717	0.899	0.662	0.916	0.790	-0.340	0.899	0.046	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
MYEENSRDNPF	0.454	0.830	0.329	0.790	0.877	-0.190	0.790	0.102	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-3	SCG2
PEFRDDGAEPGPRE(-.98)	0.266	0.751	0.429	0.790	0.623	-0.682	0.751	0.125	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Q(-17.03)EPGAPAAGM	0.216	0.751	0.537	0.901	0.720	-0.474	0.751	0.125	tr|I3MIV6|I3MIV6_ICTTR	Carboxypeptidase E	CPE
Q(-17.03)HWSYGLRPG(-.98)	0.269	0.751	0.329	0.790	1.603	0.681	0.751	0.125	tr|I3MCA0|I3MCA0_ICTTR	Progonadoliberin-1	GNRH1
Q(-17.03)KIAEKFSQ	0.371	0.775	0.329	0.790	1.345	0.428	0.775	0.111	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)KIAEKFSQR(-.98)	0.527	0.851	0.662	0.916	0.650	-0.623	0.851	0.070	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)LEDEAKELQ	0.272	0.751	0.537	0.901	0.657	-0.606	0.751	0.125	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
Q(-17.03)YDRVAELDQLLHY	0.932	0.974	0.429	0.790	1.122	0.166	0.790	0.102	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
QYDRVAELDQLLHY	0.256	0.751	0.247	0.790	0.620	-0.689	0.751	0.125	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPVKVYPNGAEDES(+79.97)AESFPLEF	0.900	0.974	0.931	0.972	1.076	0.105	0.972	0.012	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RPVKVYPNGAEDESAESFPLEF	0.292	0.751	0.329	0.790	2.186	1.128	0.751	0.125	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RTLYGFGG	0.715	0.899	0.792	0.955	1.101	0.138	0.899	0.046	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
RVLTEEEEKELENL	0.907	0.974	0.537	0.901	0.997	-0.004	0.901	0.045	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
S(+42.01)YSMEHFRWGKPV(-.98)	0.114	0.751	0.177	0.790	0.663	-0.593	0.751	0.125	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SANSNPAM(+15.99)APRE	0.114	0.751	0.126	0.787	0.492	-1.023	0.751	0.125	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SANSNPAMAPRE	0.042	0.751	0.082	0.787	0.376	-1.413	0.751	0.125	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SLDSPAGPA	0.007	0.628	0.017	0.543	0.359	-1.476	0.543	0.266	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SLDSPAGPAE	0.646	0.882	0.792	0.955	0.496	-1.013	0.882	0.055	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SPQLEDE	0.041	0.751	0.017	0.543	0.203	-2.298	0.543	0.266	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKEL	0.270	0.751	0.177	0.790	0.551	-0.860	0.751	0.125	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.227	0.751	0.247	0.790	0.651	-0.618	0.751	0.125	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SQGGEPGAYLTPDT	0.482	0.830	0.537	0.901	1.089	0.123	0.830	0.081	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQGGEPGAYLTPDTREE	0.651	0.882	0.662	0.916	1.082	0.114	0.882	0.055	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQTPLVTLF	0.332	0.751	0.662	0.916	1.165	0.221	0.751	0.125	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SQTPLVTLFKNAIIKNAHKKGQ	0.049	0.751	0.030	0.570	0.353	-1.501	0.570	0.244	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SSQEGNPPSEERGHTLQEPEEAKVGE	0.487	0.830	0.662	0.916	0.783	-0.352	0.830	0.081	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SVNPYLQGQRL	0.303	0.751	0.329	0.790	1.175	0.233	0.751	0.125	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B2	SCG5
SVNPYLQGQRLDNVV	0.224	0.751	0.662	0.916	0.540	-0.888	0.751	0.125	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B3	SCG5
SVNPYLQGQRLDNVVA	0.880	0.974	0.792	0.955	0.934	-0.099	0.955	0.020	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B4	SCG5
SVSTVLTSKYR	0.956	0.978	0.792	0.955	0.865	-0.209	0.955	0.020	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SYSMEHF	0.292	0.751	0.429	0.790	0.747	-0.421	0.751	0.125	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SYSMEHFRWGKPV(-.98)	0.495	0.830	0.662	0.916	0.827	-0.274	0.830	0.081	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
TLGGSQDKSLHN	0.563	0.865	1.000	1.000	0.992	-0.011	0.865	0.063	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-4	SCG3
TLYGFGG	0.230	0.751	0.429	0.790	0.596	-0.747	0.751	0.125	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TNEIVEEQYTPQSL	0.343	0.751	0.429	0.790	0.702	-0.511	0.751	0.125	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-4	SCG2
TPLVTLFKNAIIKNAHKKGQ	0.168	0.751	0.247	0.790	0.438	-1.193	0.751	0.125	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
VAELDQLLHY	0.472	0.830	0.247	0.790	1.206	0.270	0.790	0.102	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
VANALSHKYH	0.478	0.830	0.429	0.790	1.544	0.627	0.790	0.102	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
VGRPEWWMDYQ	0.110	0.751	0.126	0.787	0.436	-1.197	0.751	0.125	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.976	0.987	1.000	1.000	0.978	-0.032	0.987	0.006	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGF	0.740	0.905	0.931	0.972	0.739	-0.437	0.905	0.043	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
Y(+42.01)GGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAH	0.620	0.882	0.931	0.972	1.459	0.545	0.882	0.055	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNA	0.252	0.751	0.329	0.790	0.706	-0.502	0.751	0.125	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	0.036	0.751	0.017	0.543	0.499	-1.003	0.543	0.266	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.522	0.851	0.792	0.955	0.845	-0.244	0.851	0.070	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YDRVAELDQLLHY	0.606	0.882	0.792	0.955	0.751	-0.414	0.882	0.055	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
YGGFM(+15.99)RF	0.276	0.751	0.329	0.790	0.553	-0.855	0.751	0.125	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)RGL	0.125	0.751	0.126	0.787	0.533	-0.907	0.751	0.125	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAHKKGQ	0.421	0.830	0.429	0.790	0.830	-0.269	0.790	0.102	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMRF	0.691	0.899	0.792	0.955	0.842	-0.248	0.899	0.046	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.156	0.751	0.126	0.787	0.588	-0.765	0.751	0.125	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMTSE	0.380	0.776	0.662	0.916	0.742	-0.430	0.776	0.110	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNA	0.095	0.751	0.126	0.787	0.583	-0.778	0.751	0.125	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAH	0.247	0.751	0.247	0.790	0.754	-0.407	0.751	0.125	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.101	0.751	0.126	0.787	1.517	0.601	0.751	0.125	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

[1] "There is no significant differentiated features between Torpor and IBA"

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

March vs October

Full stat

Code

contrast = combo_list[[8]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: March over October"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
AADQDLGPEAPPEGVLGA	0.148	0.268	0.200	0.318	0.756	-0.403	0.268	0.572	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.107	0.218	0.114	0.223	0.574	-0.802	0.218	0.661	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AAMDLEL	0.518	0.667	0.370	0.520	1.144	0.194	0.520	0.284	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AELDQLLHY	0.224	0.356	0.236	0.363	0.606	-0.723	0.356	0.449	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AFGPRGPGLQL	0.212	0.350	0.139	0.256	0.706	-0.502	0.256	0.592	tr|I3MMW2|I3MMW2_ICTTR	Chromogranin-A	CHGA
AGAPEPAEPMELAKPSA	0.011	0.044	0.021	0.072	0.232	-2.108	0.044	1.361	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
ATLESVFQELGKLTGPSSQKRE	0.661	0.758	0.888	0.928	1.133	0.180	0.758	0.121	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-2	SCG2
DDGPYRMEHFRWGSPPKD	0.001	0.012	0.001	0.009	0.309	-1.696	0.009	2.032	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
EDREEASLQDRQYASHHT	0.270	0.410	0.114	0.223	0.654	-0.613	0.223	0.651	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EDREEASLQDRQYASHHTTE	0.000	0.004	0.001	0.006	0.329	-1.604	0.004	2.397	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHT	0.225	0.356	0.321	0.472	0.674	-0.569	0.356	0.449	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHTTE	0.023	0.081	0.021	0.072	0.611	-0.712	0.072	1.143	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EESEESEEGTTSEVT	0.015	0.056	0.021	0.072	2.234	1.159	0.056	1.254	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EIGDEENSAKFPI(-.98)	0.769	0.831	0.888	0.928	1.033	0.047	0.831	0.080	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
ELDQLLHY	0.626	0.744	0.743	0.862	1.147	0.197	0.744	0.129	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FKNAIIKNAH	0.136	0.262	0.200	0.318	0.572	-0.807	0.262	0.582	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FKNAIIKNAHKKGQ	0.632	0.744	0.673	0.832	1.365	0.449	0.744	0.129	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FLGEAYHHVPE	0.004	0.019	0.004	0.020	0.355	-1.495	0.019	1.726	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPES	0.285	0.426	0.541	0.727	0.809	-0.306	0.426	0.371	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQ	0.038	0.116	0.059	0.150	0.658	-0.603	0.116	0.937	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.000	0.001	0.000	0.004	0.272	-1.877	0.001	2.959	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRDKA	0.010	0.042	0.021	0.072	0.482	-1.053	0.042	1.381	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FPTLGGSQDKSLHN	0.000	0.001	0.000	0.004	0.595	-0.750	0.001	2.952	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-3	SCG3
GEAYHHVPESQRD	0.103	0.216	0.167	0.291	0.769	-0.380	0.216	0.665	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GEAYHHVPESQRDKA	0.027	0.086	0.074	0.175	0.577	-0.792	0.086	1.066	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GGFMRGL	0.709	0.798	0.888	0.928	0.875	-0.193	0.798	0.098	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GGPEFRDDGAEPGPRE(-.98)	0.103	0.216	0.027	0.092	0.636	-0.652	0.092	1.036	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GPEFRDDGAEPGPRE(-.98)	0.004	0.019	0.004	0.020	0.594	-0.751	0.019	1.727	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GRTLYGFGG	0.501	0.662	0.673	0.832	0.830	-0.270	0.662	0.179	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
GVANALSHKYH	0.146	0.268	0.139	0.256	0.392	-1.352	0.256	0.592	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
GVLFNPYYDPLQWKSSRFE	0.069	0.174	0.059	0.150	0.535	-0.902	0.150	0.822	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
KVVAGVANALSHKYH	0.004	0.019	0.006	0.025	0.569	-0.814	0.019	1.727	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
KYVMGHFRWD	0.055	0.148	0.036	0.113	0.563	-0.829	0.113	0.948	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
KYVMGHFRWDRF(-.98)	0.000	0.002	0.000	0.004	0.251	-1.993	0.002	2.745	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
LAGAPEPA	0.941	0.951	0.888	0.928	0.619	-0.691	0.928	0.033	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
LDQLLHY	0.005	0.023	0.002	0.017	0.507	-0.979	0.017	1.781	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LENPQPQAPARRLLPP	0.021	0.076	0.114	0.223	0.550	-0.861	0.076	1.118	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGEAYHHVPESQRD	0.000	0.001	0.000	0.004	0.252	-1.990	0.001	2.952	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LGVLFNPYYDPLQWKSSRFE	0.731	0.808	0.673	0.832	0.768	-0.381	0.808	0.093	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
MYEENSRDNPF	0.792	0.836	0.743	0.862	0.918	-0.124	0.836	0.078	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-3	SCG2
PEFRDDGAEPGPRE(-.98)	0.004	0.019	0.002	0.012	0.557	-0.844	0.012	1.912	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Q(-17.03)EPGAPAAGM	0.431	0.605	0.606	0.802	1.124	0.169	0.605	0.218	tr|I3MIV6|I3MIV6_ICTTR	Carboxypeptidase E	CPE
Q(-17.03)HWSYGLRPG(-.98)	0.003	0.019	0.006	0.025	0.494	-1.019	0.019	1.727	tr|I3MCA0|I3MCA0_ICTTR	Progonadoliberin-1	GNRH1
Q(-17.03)KIAEKFSQ	0.092	0.207	0.200	0.318	0.758	-0.401	0.207	0.685	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)KIAEKFSQR(-.98)	0.000	0.002	0.000	0.004	0.313	-1.674	0.002	2.745	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)LEDEAKELQ	0.082	0.193	0.046	0.132	0.551	-0.859	0.132	0.879	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
Q(-17.03)YDRVAELDQLLHY	0.163	0.284	0.139	0.256	0.661	-0.596	0.256	0.592	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
QYDRVAELDQLLHY	0.545	0.693	0.963	0.963	0.948	-0.077	0.693	0.159	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPVKVYPNGAEDES(+79.97)AESFPLEF	0.125	0.244	0.011	0.045	1.912	0.935	0.045	1.343	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RPVKVYPNGAEDESAESFPLEF	0.461	0.627	0.370	0.520	1.101	0.138	0.520	0.284	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RTLYGFGG	0.713	0.798	0.963	0.963	0.916	-0.126	0.798	0.098	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
RVLTEEEEKELENL	0.936	0.951	0.963	0.963	1.088	0.122	0.951	0.022	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
S(+42.01)YSMEHFRWGKPV(-.98)	0.000	0.004	0.002	0.012	0.316	-1.663	0.004	2.397	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SANSNPAM(+15.99)APRE	0.227	0.356	0.370	0.520	1.318	0.399	0.356	0.449	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SANSNPAMAPRE	0.026	0.086	0.046	0.132	0.567	-0.819	0.086	1.066	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SLDSPAGPA	0.568	0.711	0.743	0.862	1.165	0.221	0.711	0.148	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SLDSPAGPAE	0.177	0.302	0.114	0.223	0.758	-0.400	0.223	0.651	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SPQLEDE	0.953	0.953	0.236	0.363	0.513	-0.962	0.363	0.440	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKEL	0.123	0.244	0.114	0.223	0.743	-0.428	0.223	0.651	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.045	0.132	0.059	0.150	0.813	-0.299	0.132	0.878	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SQGGEPGAYLTPDT	0.322	0.474	0.277	0.419	0.737	-0.440	0.419	0.377	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQGGEPGAYLTPDTREE	0.070	0.174	0.074	0.175	0.761	-0.395	0.174	0.760	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQTPLVTLF	0.099	0.216	0.167	0.291	1.719	0.781	0.216	0.665	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SQTPLVTLFKNAIIKNAHKKGQ	0.404	0.575	0.321	0.472	0.435	-1.200	0.472	0.326	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SSQEGNPPSEERGHTLQEPEEAKVGE	0.002	0.012	0.002	0.017	0.482	-1.053	0.012	1.908	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SVNPYLQGQRL	0.002	0.015	0.004	0.020	0.309	-1.695	0.015	1.812	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B2	SCG5
SVNPYLQGQRLDNVV	0.787	0.836	0.743	0.862	1.018	0.026	0.836	0.078	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B3	SCG5
SVNPYLQGQRLDNVVA	0.048	0.134	0.074	0.175	0.662	-0.596	0.134	0.874	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B4	SCG5
SVSTVLTSKYR	0.633	0.744	0.673	0.832	0.845	-0.243	0.744	0.129	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SYSMEHF	0.844	0.882	0.888	0.928	1.042	0.059	0.882	0.055	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SYSMEHFRWGKPV(-.98)	0.000	0.002	0.000	0.004	0.213	-2.231	0.002	2.745	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
TLGGSQDKSLHN	0.033	0.102	0.036	0.113	0.680	-0.557	0.102	0.992	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-4	SCG3
TLYGFGG	0.769	0.831	0.541	0.727	0.894	-0.161	0.727	0.138	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TNEIVEEQYTPQSL	0.936	0.951	0.888	0.928	0.933	-0.100	0.928	0.033	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-4	SCG2
TPLVTLFKNAIIKNAHKKGQ	0.398	0.575	0.888	0.928	0.507	-0.980	0.575	0.240	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
VAELDQLLHY	0.651	0.755	0.815	0.923	0.918	-0.123	0.755	0.122	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
VANALSHKYH	0.058	0.152	0.093	0.203	0.416	-1.266	0.152	0.818	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
VGRPEWWMDYQ	0.141	0.265	0.093	0.203	1.376	0.461	0.203	0.693	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.240	0.369	0.167	0.291	0.752	-0.412	0.291	0.536	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGF	0.087	0.200	0.059	0.150	0.661	-0.597	0.150	0.822	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
Y(+42.01)GGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAH	0.014	0.054	0.011	0.045	0.463	-1.111	0.045	1.343	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNA	0.450	0.622	0.815	0.923	0.894	-0.162	0.622	0.206	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	0.000	0.002	0.000	0.004	0.245	-2.029	0.002	2.745	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.000	0.004	0.000	0.004	0.273	-1.873	0.004	2.424	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YDRVAELDQLLHY	0.575	0.711	0.541	0.727	1.179	0.237	0.711	0.148	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
YGGFM(+15.99)RF	0.003	0.019	0.006	0.025	1.682	0.750	0.019	1.727	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)RGL	0.048	0.134	0.046	0.132	1.390	0.475	0.132	0.879	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAHKKGQ	0.507	0.662	0.963	0.963	0.971	-0.043	0.662	0.179	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMRF	0.072	0.174	0.093	0.203	0.642	-0.640	0.174	0.760	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.003	0.019	0.006	0.025	0.446	-1.164	0.019	1.727	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMTSE	0.190	0.319	0.200	0.318	0.685	-0.546	0.318	0.498	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNA	0.598	0.730	0.743	0.862	0.877	-0.189	0.730	0.137	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAH	0.487	0.654	0.673	0.832	1.040	0.057	0.654	0.185	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.158	0.280	0.200	0.318	0.693	-0.529	0.280	0.553	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	status	Accession	Name	GN
DDGPYRMEHFRWGSPPKD	0.001	0.012	0.001	0.009	0.309	-1.696	0.009	2.032	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
EDREEASLQDRQYASHHTTE	0.000	0.004	0.001	0.006	0.329	-1.604	0.004	2.397	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPE	0.004	0.019	0.004	0.020	0.355	-1.495	0.019	1.726	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.000	0.001	0.000	0.004	0.272	-1.877	0.001	2.959	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FPTLGGSQDKSLHN	0.000	0.001	0.000	0.004	0.595	-0.750	0.001	2.952	Down	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-3	SCG3
GPEFRDDGAEPGPRE(-.98)	0.004	0.019	0.004	0.020	0.594	-0.751	0.019	1.727	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
KVVAGVANALSHKYH	0.004	0.019	0.006	0.025	0.569	-0.814	0.019	1.727	Down	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
KYVMGHFRWDRF(-.98)	0.000	0.002	0.000	0.004	0.251	-1.993	0.002	2.745	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
LDQLLHY	0.005	0.023	0.002	0.017	0.507	-0.979	0.017	1.781	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LGEAYHHVPESQRD	0.000	0.001	0.000	0.004	0.252	-1.990	0.001	2.952	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
PEFRDDGAEPGPRE(-.98)	0.004	0.019	0.002	0.012	0.557	-0.844	0.012	1.912	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Q(-17.03)HWSYGLRPG(-.98)	0.003	0.019	0.006	0.025	0.494	-1.019	0.019	1.727	Down	tr|I3MCA0|I3MCA0_ICTTR	Progonadoliberin-1	GNRH1
Q(-17.03)KIAEKFSQR(-.98)	0.000	0.002	0.000	0.004	0.313	-1.674	0.002	2.745	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
S(+42.01)YSMEHFRWGKPV(-.98)	0.000	0.004	0.002	0.012	0.316	-1.663	0.004	2.397	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SSQEGNPPSEERGHTLQEPEEAKVGE	0.002	0.012	0.002	0.017	0.482	-1.053	0.012	1.908	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SVNPYLQGQRL	0.002	0.015	0.004	0.020	0.309	-1.695	0.015	1.812	Down	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B2	SCG5
SYSMEHFRWGKPV(-.98)	0.000	0.002	0.000	0.004	0.213	-2.231	0.002	2.745	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	0.000	0.002	0.000	0.004	0.245	-2.029	0.002	2.745	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.000	0.004	0.000	0.004	0.273	-1.873	0.004	2.424	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFM(+15.99)RF	0.003	0.019	0.006	0.025	1.682	0.750	0.019	1.727	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.003	0.019	0.006	0.025	0.446	-1.164	0.019	1.727	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

March vs Torpor

Full stat

Code

contrast = combo_list[[9]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: March over Torpor"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
AADQDLGPEAPPEGVLGA	0.171	0.281	0.284	0.387	0.659	-0.603	0.281	0.551	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.006	0.030	0.006	0.027	0.241	-2.051	0.027	1.576	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AAMDLEL	0.143	0.240	0.127	0.226	0.487	-1.037	0.226	0.646	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AELDQLLHY	0.312	0.451	0.284	0.387	0.609	-0.716	0.387	0.412	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AFGPRGPGLQL	0.028	0.083	0.030	0.082	0.551	-0.861	0.082	1.088	tr|I3MMW2|I3MMW2_ICTTR	Chromogranin-A	CHGA
AGAPEPAEPMELAKPSA	0.085	0.181	0.171	0.272	0.287	-1.803	0.181	0.743	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
ATLESVFQELGKLTGPSSQKRE	0.407	0.533	0.524	0.656	0.867	-0.206	0.533	0.273	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-2	SCG2
DDGPYRMEHFRWGSPPKD	0.091	0.185	0.171	0.272	0.540	-0.888	0.185	0.733	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
EDREEASLQDRQYASHHT	0.555	0.687	0.354	0.469	0.739	-0.435	0.469	0.329	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EDREEASLQDRQYASHHTTE	0.137	0.238	0.127	0.226	0.616	-0.699	0.226	0.646	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHT	0.591	0.712	1.000	1.000	1.177	0.235	0.712	0.148	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHTTE	0.339	0.479	0.284	0.387	0.786	-0.347	0.387	0.412	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EESEESEEGTTSEVT	0.071	0.158	0.127	0.226	2.496	1.320	0.158	0.800	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EIGDEENSAKFPI(-.98)	0.807	0.848	0.943	0.953	0.855	-0.226	0.848	0.072	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
ELDQLLHY	0.948	0.958	0.622	0.730	0.995	-0.007	0.730	0.136	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FKNAIIKNAH	0.660	0.775	0.943	0.953	0.791	-0.338	0.775	0.110	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FKNAIIKNAHKKGQ	0.137	0.238	0.222	0.332	1.544	0.626	0.238	0.624	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FLGEAYHHVPE	0.089	0.185	0.093	0.191	0.533	-0.909	0.185	0.733	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPES	0.731	0.828	0.943	0.953	1.125	0.169	0.828	0.082	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQ	0.587	0.712	0.833	0.900	0.883	-0.180	0.712	0.148	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.000	0.006	0.002	0.012	0.341	-1.553	0.006	2.198	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRDKA	0.001	0.009	0.002	0.012	0.362	-1.467	0.009	2.027	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FPTLGGSQDKSLHN	0.004	0.024	0.002	0.012	0.456	-1.133	0.012	1.915	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-3	SCG3
GEAYHHVPESQRD	0.642	0.764	0.127	0.226	0.967	-0.048	0.226	0.646	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GEAYHHVPESQRDKA	0.121	0.227	0.127	0.226	0.619	-0.693	0.226	0.646	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GGFMRGL	0.942	0.958	0.943	0.953	1.193	0.255	0.953	0.021	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GGPEFRDDGAEPGPRE(-.98)	0.002	0.017	0.011	0.044	0.289	-1.793	0.017	1.775	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GPEFRDDGAEPGPRE(-.98)	0.002	0.016	0.002	0.012	0.219	-2.188	0.012	1.915	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GRTLYGFGG	0.036	0.094	0.030	0.082	0.457	-1.130	0.082	1.088	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
GVANALSHKYH	0.414	0.533	0.622	0.730	0.500	-1.000	0.533	0.273	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
GVLFNPYYDPLQWKSSRFE	0.061	0.140	0.065	0.153	0.422	-1.243	0.140	0.855	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
KVVAGVANALSHKYH	0.007	0.033	0.003	0.018	0.445	-1.170	0.018	1.739	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
KYVMGHFRWD	0.461	0.578	0.622	0.730	0.758	-0.400	0.578	0.238	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
KYVMGHFRWDRF(-.98)	0.007	0.033	0.019	0.060	0.428	-1.223	0.033	1.483	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
LAGAPEPA	0.015	0.055	0.045	0.114	2.587	1.371	0.055	1.262	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
LDQLLHY	0.092	0.185	0.127	0.226	0.572	-0.806	0.185	0.733	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LENPQPQAPARRLLPP	0.120	0.227	0.171	0.272	0.615	-0.700	0.227	0.643	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGEAYHHVPESQRD	0.000	0.001	0.002	0.012	0.296	-1.754	0.001	2.941	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LGVLFNPYYDPLQWKSSRFE	0.013	0.049	0.045	0.114	0.230	-2.120	0.049	1.313	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
MYEENSRDNPF	0.258	0.385	0.284	0.387	0.748	-0.418	0.385	0.414	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-3	SCG2
PEFRDDGAEPGPRE(-.98)	0.003	0.019	0.002	0.012	0.271	-1.882	0.012	1.915	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Q(-17.03)EPGAPAAGM	0.401	0.533	0.030	0.082	0.660	-0.599	0.082	1.088	tr|I3MIV6|I3MIV6_ICTTR	Carboxypeptidase E	CPE
Q(-17.03)HWSYGLRPG(-.98)	0.012	0.049	0.002	0.012	0.352	-1.506	0.012	1.915	tr|I3MCA0|I3MCA0_ICTTR	Progonadoliberin-1	GNRH1
Q(-17.03)KIAEKFSQ	0.777	0.848	0.724	0.830	1.134	0.182	0.830	0.081	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)KIAEKFSQR(-.98)	0.001	0.016	0.003	0.018	0.432	-1.211	0.016	1.804	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)LEDEAKELQ	0.054	0.126	0.093	0.191	0.423	-1.242	0.126	0.900	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
Q(-17.03)YDRVAELDQLLHY	0.003	0.019	0.006	0.027	0.178	-2.488	0.019	1.719	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
QYDRVAELDQLLHY	0.715	0.820	0.284	0.387	0.465	-1.105	0.387	0.412	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPVKVYPNGAEDES(+79.97)AESFPLEF	0.384	0.531	0.833	0.900	1.176	0.234	0.531	0.275	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RPVKVYPNGAEDESAESFPLEF	0.805	0.848	0.943	0.953	1.353	0.436	0.848	0.072	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RTLYGFGG	0.019	0.063	0.019	0.060	0.421	-1.249	0.060	1.219	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
RVLTEEEEKELENL	0.409	0.533	0.833	0.900	1.097	0.134	0.533	0.273	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
S(+42.01)YSMEHFRWGKPV(-.98)	0.000	0.009	0.003	0.018	0.509	-0.973	0.009	2.037	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SANSNPAM(+15.99)APRE	0.342	0.479	0.284	0.387	0.590	-0.761	0.387	0.412	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SANSNPAMAPRE	0.000	0.000	0.002	0.012	0.112	-3.159	0.000	3.513	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SLDSPAGPA	0.020	0.063	0.093	0.191	0.285	-1.812	0.063	1.202	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SLDSPAGPAE	0.126	0.232	0.065	0.153	0.484	-1.045	0.153	0.814	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SPQLEDE	0.037	0.094	0.006	0.027	0.132	-2.922	0.027	1.576	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKEL	0.005	0.028	0.002	0.012	0.206	-2.278	0.012	1.915	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.143	0.240	0.093	0.191	0.676	-0.565	0.191	0.720	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SQGGEPGAYLTPDT	0.846	0.874	0.833	0.900	0.854	-0.227	0.874	0.059	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQGGEPGAYLTPDTREE	0.075	0.163	0.171	0.272	0.702	-0.510	0.163	0.788	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQTPLVTLF	0.783	0.848	0.524	0.656	0.923	-0.115	0.656	0.183	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SQTPLVTLFKNAIIKNAHKKGQ	0.009	0.039	0.006	0.027	0.094	-3.416	0.027	1.576	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SSQEGNPPSEERGHTLQEPEEAKVGE	0.097	0.189	0.093	0.191	0.651	-0.618	0.189	0.723	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SVNPYLQGQRL	0.019	0.063	0.045	0.114	0.420	-1.251	0.063	1.202	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B2	SCG5
SVNPYLQGQRLDNVV	0.044	0.109	0.019	0.060	0.256	-1.966	0.060	1.219	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B3	SCG5
SVNPYLQGQRLDNVVA	0.000	0.006	0.002	0.012	0.322	-1.635	0.006	2.198	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B4	SCG5
SVSTVLTSKYR	0.174	0.282	0.222	0.332	0.552	-0.858	0.282	0.550	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SYSMEHF	0.035	0.094	0.019	0.060	0.616	-0.699	0.060	1.219	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SYSMEHFRWGKPV(-.98)	0.020	0.063	0.030	0.082	0.431	-1.215	0.063	1.202	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
TLGGSQDKSLHN	0.013	0.049	0.006	0.027	0.533	-0.908	0.027	1.576	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-4	SCG3
TLYGFGG	0.136	0.238	0.171	0.272	0.384	-1.382	0.238	0.624	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TNEIVEEQYTPQSL	0.258	0.385	0.222	0.332	0.622	-0.685	0.332	0.479	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-4	SCG2
TPLVTLFKNAIIKNAHKKGQ	0.036	0.094	0.093	0.191	0.182	-2.458	0.094	1.028	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
VAELDQLLHY	0.749	0.838	0.622	0.730	0.692	-0.530	0.730	0.136	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
VANALSHKYH	0.214	0.336	0.222	0.332	0.519	-0.945	0.332	0.479	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
VGRPEWWMDYQ	0.047	0.114	0.030	0.082	0.398	-1.329	0.082	1.088	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.696	0.808	0.622	0.730	0.871	-0.199	0.730	0.136	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGF	0.002	0.017	0.006	0.027	0.328	-1.607	0.017	1.775	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
Y(+42.01)GGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAH	0.988	0.988	0.943	0.953	1.109	0.150	0.953	0.021	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNA	0.812	0.848	0.724	0.830	1.078	0.109	0.830	0.081	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	0.002	0.016	0.003	0.018	0.410	-1.285	0.016	1.793	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.794	0.848	0.833	0.900	0.931	-0.103	0.848	0.072	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YDRVAELDQLLHY	0.005	0.028	0.019	0.060	0.322	-1.634	0.028	1.549	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
YGGFM(+15.99)RF	0.258	0.385	0.127	0.226	0.803	-0.317	0.226	0.646	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)RGL	0.196	0.312	0.171	0.272	0.692	-0.531	0.272	0.565	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAHKKGQ	0.413	0.533	0.435	0.568	0.530	-0.917	0.533	0.273	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMRF	0.002	0.016	0.002	0.012	0.286	-1.805	0.012	1.915	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.001	0.016	0.002	0.012	0.201	-2.313	0.012	1.915	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMTSE	0.032	0.092	0.065	0.153	0.489	-1.032	0.092	1.036	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNA	0.028	0.083	0.019	0.060	0.418	-1.260	0.060	1.219	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAH	0.265	0.389	0.524	0.656	1.346	0.429	0.389	0.410	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.424	0.539	0.354	0.469	0.778	-0.363	0.469	0.329	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	status	Accession	Name	GN
AADQDLGPEAPPEGVLGAL	0.006	0.030	0.006	0.027	0.241	-2.051	0.027	1.576	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
FLGEAYHHVPESQRD	0.000	0.006	0.002	0.012	0.341	-1.553	0.006	2.198	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRDKA	0.001	0.009	0.002	0.012	0.362	-1.467	0.009	2.027	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FPTLGGSQDKSLHN	0.004	0.024	0.002	0.012	0.456	-1.133	0.012	1.915	Down	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-3	SCG3
GGPEFRDDGAEPGPRE(-.98)	0.002	0.017	0.011	0.044	0.289	-1.793	0.017	1.775	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GPEFRDDGAEPGPRE(-.98)	0.002	0.016	0.002	0.012	0.219	-2.188	0.012	1.915	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
KVVAGVANALSHKYH	0.007	0.033	0.003	0.018	0.445	-1.170	0.018	1.739	Down	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
LGEAYHHVPESQRD	0.000	0.001	0.002	0.012	0.296	-1.754	0.001	2.941	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
PEFRDDGAEPGPRE(-.98)	0.003	0.019	0.002	0.012	0.271	-1.882	0.012	1.915	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Q(-17.03)HWSYGLRPG(-.98)	0.012	0.049	0.002	0.012	0.352	-1.506	0.012	1.915	Down	tr|I3MCA0|I3MCA0_ICTTR	Progonadoliberin-1	GNRH1
Q(-17.03)KIAEKFSQR(-.98)	0.001	0.016	0.003	0.018	0.432	-1.211	0.016	1.804	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)YDRVAELDQLLHY	0.003	0.019	0.006	0.027	0.178	-2.488	0.019	1.719	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
S(+42.01)YSMEHFRWGKPV(-.98)	0.000	0.009	0.003	0.018	0.509	-0.973	0.009	2.037	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SANSNPAMAPRE	0.000	0.000	0.002	0.012	0.112	-3.159	0.000	3.513	Down	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SPQLEDEAKEL	0.005	0.028	0.002	0.012	0.206	-2.278	0.012	1.915	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SQTPLVTLFKNAIIKNAHKKGQ	0.009	0.039	0.006	0.027	0.094	-3.416	0.027	1.576	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SVNPYLQGQRLDNVVA	0.000	0.006	0.002	0.012	0.322	-1.635	0.006	2.198	Down	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B4	SCG5
TLGGSQDKSLHN	0.013	0.049	0.006	0.027	0.533	-0.908	0.027	1.576	Down	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-4	SCG3
VKVGVNGF	0.002	0.017	0.006	0.027	0.328	-1.607	0.017	1.775	Down	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	0.002	0.016	0.003	0.018	0.410	-1.285	0.016	1.793	Down	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMRF	0.002	0.016	0.002	0.012	0.286	-1.805	0.012	1.915	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.001	0.016	0.002	0.012	0.201	-2.313	0.012	1.915	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

October vs Torpor

Full stat

Code

contrast = combo_list[[10]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: October over Torpor"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
AADQDLGPEAPPEGVLGA	0.431	0.588	0.438	0.548	0.871	-0.200	0.548	0.261	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.099	0.245	0.083	0.229	0.421	-1.249	0.229	0.640	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AAMDLEL	0.282	0.435	0.147	0.345	0.426	-1.231	0.345	0.462	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AELDQLLHY	0.794	0.829	0.699	0.783	1.005	0.007	0.783	0.106	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
AFGPRGPGLQL	0.971	0.971	0.190	0.372	0.780	-0.358	0.372	0.430	tr|I3MMW2|I3MMW2_ICTTR	Chromogranin-A	CHGA
AGAPEPAEPMELAKPSA	0.648	0.752	0.898	0.938	1.236	0.305	0.752	0.124	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
ATLESVFQELGKLTGPSSQKRE	0.321	0.464	0.298	0.437	0.766	-0.385	0.437	0.359	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-2	SCG2
DDGPYRMEHFRWGSPPKD	0.011	0.108	0.019	0.081	1.751	0.808	0.081	1.091	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
EDREEASLQDRQYASHHT	0.551	0.682	0.699	0.783	1.131	0.177	0.682	0.166	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EDREEASLQDRQYASHHTTE	0.055	0.180	0.029	0.105	1.873	0.905	0.105	0.980	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHT	0.120	0.262	0.060	0.176	1.746	0.804	0.176	0.754	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EEASLQDRQYASHHTTE	0.281	0.435	0.298	0.437	1.287	0.364	0.435	0.361	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EESEESEEGTTSEVT	0.933	0.943	0.898	0.938	1.118	0.160	0.938	0.028	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
EIGDEENSAKFPI(-.98)	0.588	0.700	0.606	0.713	0.827	-0.274	0.700	0.155	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
ELDQLLHY	0.666	0.764	0.438	0.548	0.868	-0.204	0.548	0.261	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FKNAIIKNAH	0.439	0.590	0.298	0.437	1.384	0.469	0.437	0.359	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FKNAIIKNAHKKGQ	0.300	0.447	0.298	0.437	1.131	0.177	0.437	0.359	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
FLGEAYHHVPE	0.195	0.364	0.364	0.488	1.501	0.586	0.364	0.439	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPES	0.275	0.435	0.190	0.372	1.390	0.475	0.372	0.430	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQ	0.162	0.332	0.190	0.372	1.342	0.424	0.332	0.479	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.201	0.364	0.298	0.437	1.252	0.324	0.364	0.439	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRDKA	0.632	0.742	0.898	0.938	0.751	-0.414	0.742	0.129	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FPTLGGSQDKSLHN	0.141	0.302	0.190	0.372	0.767	-0.383	0.302	0.520	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-3	SCG3
GEAYHHVPESQRD	0.483	0.618	0.898	0.938	1.259	0.332	0.618	0.209	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GEAYHHVPESQRDKA	0.779	0.822	0.606	0.713	1.071	0.099	0.713	0.147	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GGFMRGL	0.762	0.814	0.518	0.641	1.364	0.448	0.641	0.193	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GGPEFRDDGAEPGPRE(-.98)	0.019	0.108	0.012	0.070	0.454	-1.140	0.070	1.152	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GPEFRDDGAEPGPRE(-.98)	0.011	0.108	0.002	0.031	0.369	-1.437	0.031	1.504	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
GRTLYGFGG	0.112	0.262	0.147	0.345	0.551	-0.860	0.262	0.582	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
GVANALSHKYH	0.724	0.792	0.699	0.783	1.276	0.352	0.783	0.106	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
GVLFNPYYDPLQWKSSRFE	0.381	0.535	0.298	0.437	0.790	-0.341	0.437	0.359	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
KVVAGVANALSHKYH	0.232	0.396	0.240	0.417	0.782	-0.355	0.396	0.402	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
KYVMGHFRWD	0.168	0.335	0.240	0.417	1.346	0.429	0.335	0.475	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
KYVMGHFRWDRF(-.98)	0.020	0.108	0.042	0.136	1.706	0.770	0.108	0.968	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
LAGAPEPA	0.000	0.015	0.001	0.023	4.176	2.062	0.015	1.825	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
LDQLLHY	0.919	0.939	1.000	1.000	1.128	0.173	0.939	0.027	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LENPQPQAPARRLLPP	0.749	0.810	1.000	1.000	1.118	0.161	0.810	0.092	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGEAYHHVPESQRD	0.192	0.364	0.438	0.548	1.178	0.236	0.364	0.439	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LGVLFNPYYDPLQWKSSRFE	0.006	0.096	0.012	0.070	0.300	-1.739	0.070	1.152	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
MYEENSRDNPF	0.308	0.452	0.298	0.437	0.816	-0.294	0.437	0.359	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-3	SCG2
PEFRDDGAEPGPRE(-.98)	0.034	0.132	0.019	0.081	0.487	-1.038	0.081	1.091	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Q(-17.03)EPGAPAAGM	0.003	0.063	0.019	0.081	0.587	-0.768	0.063	1.198	tr|I3MIV6|I3MIV6_ICTTR	Carboxypeptidase E	CPE
Q(-17.03)HWSYGLRPG(-.98)	0.271	0.435	0.364	0.488	0.713	-0.487	0.435	0.361	tr|I3MCA0|I3MCA0_ICTTR	Progonadoliberin-1	GNRH1
Q(-17.03)KIAEKFSQ	0.228	0.396	0.190	0.372	1.498	0.583	0.372	0.430	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)KIAEKFSQR(-.98)	0.099	0.245	0.364	0.488	1.378	0.463	0.245	0.611	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
Q(-17.03)LEDEAKELQ	0.451	0.590	0.606	0.713	0.767	-0.383	0.590	0.229	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
Q(-17.03)YDRVAELDQLLHY	0.022	0.108	0.019	0.081	0.269	-1.892	0.081	1.091	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
QYDRVAELDQLLHY	0.156	0.325	0.240	0.417	0.490	-1.028	0.325	0.487	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPVKVYPNGAEDES(+79.97)AESFPLEF	0.114	0.262	0.112	0.284	0.615	-0.701	0.262	0.582	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RPVKVYPNGAEDESAESFPLEF	0.884	0.913	1.000	1.000	1.230	0.298	0.913	0.040	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
RTLYGFGG	0.031	0.126	0.029	0.105	0.459	-1.123	0.105	0.980	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
RVLTEEEEKELENL	0.452	0.590	0.364	0.488	1.009	0.012	0.488	0.311	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
S(+42.01)YSMEHFRWGKPV(-.98)	0.020	0.108	0.019	0.081	1.614	0.690	0.081	1.091	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SANSNPAM(+15.99)APRE	0.080	0.220	0.112	0.284	0.448	-1.160	0.220	0.658	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SANSNPAMAPRE	0.000	0.003	0.001	0.023	0.197	-2.340	0.003	2.469	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
SLDSPAGPA	0.001	0.032	0.007	0.060	0.244	-2.032	0.032	1.500	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SLDSPAGPAE	0.575	0.693	0.699	0.783	0.639	-0.646	0.693	0.159	tr|I3M5J1|I3M5J1_ICTTR	Corticoliberin	CRH
SPQLEDE	0.040	0.139	0.001	0.023	0.257	-1.960	0.023	1.629	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKEL	0.012	0.108	0.002	0.031	0.277	-1.851	0.031	1.504	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.344	0.491	0.298	0.437	0.831	-0.266	0.437	0.359	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SQGGEPGAYLTPDT	0.226	0.396	0.298	0.437	1.159	0.213	0.396	0.402	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQGGEPGAYLTPDTREE	0.677	0.767	0.606	0.713	0.924	-0.115	0.713	0.147	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SQTPLVTLF	0.118	0.262	0.240	0.417	0.537	-0.897	0.262	0.581	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SQTPLVTLFKNAIIKNAHKKGQ	0.021	0.108	0.007	0.060	0.215	-2.216	0.060	1.224	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SSQEGNPPSEERGHTLQEPEEAKVGE	0.196	0.364	0.298	0.437	1.351	0.434	0.364	0.439	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SVNPYLQGQRL	0.074	0.212	0.190	0.372	1.360	0.444	0.212	0.674	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B2	SCG5
SVNPYLQGQRLDNVV	0.035	0.133	0.001	0.023	0.251	-1.993	0.023	1.629	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B3	SCG5
SVNPYLQGQRLDNVVA	0.008	0.101	0.012	0.070	0.487	-1.039	0.070	1.152	tr|I3MEQ9|I3MEQ9_ICTTR	Neuroendocrine protein 7B4	SCG5
SVSTVLTSKYR	0.300	0.447	0.364	0.488	0.653	-0.615	0.447	0.350	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SYSMEHF	0.027	0.116	0.019	0.081	0.591	-0.758	0.081	1.091	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
SYSMEHFRWGKPV(-.98)	0.023	0.108	0.042	0.136	2.022	1.016	0.108	0.968	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
TLGGSQDKSLHN	0.533	0.668	0.797	0.882	0.784	-0.352	0.668	0.175	tr|I3MPL6|I3MPL6_ICTTR	Secretogranin-4	SCG3
TLYGFGG	0.090	0.241	0.112	0.284	0.429	-1.220	0.241	0.618	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TNEIVEEQYTPQSL	0.266	0.435	0.190	0.372	0.667	-0.585	0.372	0.430	tr|I3N6V4|I3N6V4_ICTTR	Secretogranin-4	SCG2
TPLVTLFKNAIIKNAHKKGQ	0.068	0.199	0.029	0.105	0.359	-1.478	0.105	0.980	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
VAELDQLLHY	0.260	0.435	0.240	0.417	0.754	-0.407	0.417	0.379	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
VANALSHKYH	0.712	0.787	0.898	0.938	1.249	0.321	0.787	0.104	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
VGRPEWWMDYQ	0.018	0.108	0.004	0.047	0.289	-1.790	0.047	1.328	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.410	0.567	0.438	0.548	1.159	0.213	0.548	0.261	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGF	0.062	0.193	0.190	0.372	0.497	-1.010	0.193	0.714	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
Y(+42.01)GGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAH	0.094	0.245	0.060	0.176	2.395	1.260	0.176	0.754	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNA	0.708	0.787	1.000	1.000	1.207	0.271	0.787	0.104	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAH	0.021	0.108	0.042	0.136	1.675	0.744	0.108	0.968	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
Y(+42.01)GGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.018	0.108	0.012	0.070	3.412	1.771	0.070	1.152	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YDRVAELDQLLHY	0.001	0.032	0.004	0.047	0.273	-1.871	0.032	1.500	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
YGGFM(+15.99)RF	0.039	0.139	0.083	0.229	0.477	-1.067	0.139	0.857	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)RGL	0.066	0.199	0.060	0.176	0.498	-1.006	0.176	0.754	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFM(+15.99)TSEKSQTPLVTLFKNAIIKNAHKKGQ	0.113	0.262	0.147	0.345	0.546	-0.874	0.262	0.582	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMRF	0.014	0.108	0.007	0.060	0.446	-1.165	0.060	1.224	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.027	0.116	0.012	0.070	0.451	-1.150	0.070	1.152	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMTSE	0.198	0.364	0.240	0.417	0.714	-0.486	0.364	0.439	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNA	0.046	0.155	0.029	0.105	0.476	-1.071	0.105	0.980	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAH	0.486	0.618	0.438	0.548	1.294	0.372	0.548	0.261	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC
YGGFMTSEKSQTPLVTLFKNAIIKNAHKKGQ	0.565	0.689	0.364	0.488	1.122	0.166	0.488	0.311	tr|I3M7B6|I3M7B6_ICTTR	Pro-opiomelanocortin	POMC

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	status	Accession	Name	GN
LAGAPEPA	0.000	0.015	0.001	0.023	4.176	2.062	0.015	1.825	Up	tr|I3MXH3|I3MXH3_ICTTR	Vasopressin-neurophysin 2-copeptin-like	AVP
SANSNPAMAPRE	0.000	0.003	0.001	0.023	0.197	-2.340	0.003	2.469	Down	tr|I3MP38|I3MP38_ICTTR	Somatostatin	SST
YDRVAELDQLLHY	0.001	0.032	0.004	0.047	0.273	-1.871	0.032	1.500	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

Multivariate analysis

All group heatmap (ordered)

Code

# for ordered column without clustering samples

# data wrangling for all group heatmap
norm_d2 = t(norm_d1) %>% as.data.frame()

norm_d3 = norm_d2 %>%
        arrange(factor(class, levels = col_order))

norm_d4 = t(norm_d3) %>% as.data.frame()
norm_d4_mod = norm_d4[-1,] %>%
        as.data.frame() %>%
        rownames_to_column(., var = "rowname") %>%
        mutate(across(-rowname, as.numeric)) %>%
        column_to_rownames(., var = "rowname")

anno <- data.frame(Label = as.factor(t(norm_d4)[, "class"]))
# levels() only change the name of each level, it doesn't reorder
# factor() to reorder factor level
anno$Label = factor(anno$Label, levels = col_order)
#levels(anno$Label)

rownames(norm_d4_mod) = feature_name$name

heatmap(norm_d4_mod, sample_anno = anno, sample_anno_col = "Label", sample_colors = anno_colors, feature_anno = feature_meta, feature_label = "Peptide", cluster_col_switch = FALSE, rowname_switch = TRUE, save = FALSE)

All group heatmap (clustered)

Code

heatmap(norm_d4_mod, sample_anno = anno, sample_anno_col = "Label", sample_colors = anno_colors, feature_anno = feature_meta, feature_label = "Peptide", cluster_col_switch = TRUE, rowname_switch = TRUE, save = FALSE)

Hypothalamus

Label-free peptidomics

Total number of samples after LC-MS: 45

• August: 9

• October: 9

• IBA: 8

• Torpor: 11

• March: 8

Total number of feature provided: 202

Three step data processing:

• Batch correction

• Log2 transformation

• EigenMS normalization

Batch correction

Batch correction using package statTarget evaluates the missing values and a feature will be kept if it has non-zero value for at least 50% of samples (statTarget default is 80%) in any one group (remove 82 features). It then imputes missing values for the present features and QC-based signal correction. At last, it removes features CV% > 50% (default, removes 12 features).

Code

pheno <- "CNS_meta4samples_hypo.csv"
dfile = "CNS_data4samples_hypo.csv"
#labels <- read.csv("CNS_label4samples_pituitary.csv", row.names = "SampleName")

statTarget::shiftCor(pheno, dfile,  QCspan = 0.25, Frule = 0.5,
                     degree = 2,imputeM = "KNN", ntree=500, coCV = 50)

statTarget: Signal Correction Start... Time: Mon Nov 20 19:26:21 2023 

* Step 1: Data File Checking Start..., Time:  Mon Nov 20 19:26:21 2023 

 Data Link 
 metaFile: CNS_meta4samples_hypo.csv 
 profileFile: CNS_data4samples_hypo.csv 

 55 Meta Samples vs 55 Profile samples
 The Meta samples list (*NA, missing data from the Profile File)

 [1] "20220217_QC1" "20220217_QC2" "Hypo_39"      "Hypo_36"      "Hypo_44"     
 [6] "20220218_QC1" "Hypo_25"      "Hypo_48"      "Hypo_52"      "Hypo_21"     
[11] "Hypo_20"      "Hypo_55"      "20220218_QC2" "Hypo_60"      "Hypo_19"     
[16] "Hypo_42"      "Hypo_37"      "Hypo_24"      "Hypo_22"      "Hypo_43"     
[21] "Hypo_35"      "Hypo_63"      "20220219_QC1" "Hypo_66"      "Hypo_54"     
[26] "Hypo_65"      "Hypo_49"      "Hypo_53"      "Hypo_23"      "Hypo_31"     
[31] "Hypo_45"      "Hypo_32"      "20220220_QC1" "Hypo_57"      "Hypo_33"     
[36] "Hypo_40"      "Hypo_47"      "Hypo_58"      "Hypo_51"      "Hypo_46"     
[41] "Hypo_64"      "Hypo_59"      "20220221_QC1" "20220223_QC1" "Hypo_27"     
[46] "Hypo_34"      "Hypo_26"      "Hypo_61"      "Hypo_38"      "Hypo_62"     
[51] "Hypo_50"      "Hypo_56"      "Hypo_41"      "20220223_QC2" "20220223_QC3"

 Meta-information: 

    Class No.
1  August   9
2     IBA   8
3   March   8
4 October   9
5      QC  10
6  Torpor  11
  Batch No.
1     1  55

 Metabolic profile information: 

               no.
QC and samples  55
Metabolites    206

* Step 2: Evaluation of Missing Value... 

 The number of missing value before QC based signal correction:  2606
 The number of filtered variables using the modified  50 % rule :   82 

* Step 3: Imputation start... 

 The imputation method was set at 'KNN'
 The number of missing value after imputation:  0
 Imputation Finished! 
 
* Step 4: QC-based Signal Correction Start... Time:  Mon Nov 20 19:26:21 2023 

 The Signal Correction method was set at QC-RFSC 

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 Calculation of CV distribution of raw peaks (QC)...

        CV<5% CV<10%  CV<15%   CV<20%   CV<25%   CV<30%   CV<35%   CV<40%
Batch_1     0      0 4.83871 13.70968 24.19355 32.25806 40.32258 52.41935
Total       0      0 4.83871 13.70968 24.19355 32.25806 40.32258 52.41935
          CV<45%   CV<50%   CV<55%   CV<60%   CV<65%   CV<70%   CV<75%   CV<80%
Batch_1 69.35484 75.80645 84.67742 87.90323 91.93548 94.35484 96.77419 97.58065
Total   69.35484 75.80645 84.67742 87.90323 91.93548 94.35484 96.77419 97.58065
          CV<85%  CV<90%   CV<95%  CV<100%
Batch_1 97.58065 98.3871 99.19355 99.19355
Total   97.58065 98.3871 99.19355 99.19355

 Calculation of CV distribution of corrected peaks (QC)...

        CV<5%   CV<10%   CV<15%   CV<20%  CV<25%   CV<30%   CV<35%   CV<40%
Batch_1     0 8.064516 20.96774 37.90323 48.3871 62.09677 72.58065 83.87097
Total       0 8.064516 20.96774 37.90323 48.3871 62.09677 72.58065 83.87097
          CV<45%   CV<50%   CV<55%   CV<60%  CV<65%   CV<70% CV<75% CV<80%
Batch_1 86.29032 90.32258 94.35484 96.77419 98.3871 99.19355    100    100
Total   86.29032 90.32258 94.35484 96.77419 98.3871 99.19355    100    100
        CV<85% CV<90% CV<95% CV<100%
Batch_1    100    100    100     100
Total      100    100    100     100

* Step 5:  Removal of the features (CV% > 50%) Mon Nov 20 19:26:22 2023 

 No. of removed features: 12
 Feature name: FVQMMTAK VAELDQLLHY Q(-17.03)EPGAPAAGM SEGPLKGILGY SNRVVDLMVHMASKE GDILGKYVD TPGVAADL Q(-17.03)LEDEAKELQ ASLKPEFVDIINAKQ FVDIINAKQ GFLVFHSFGGG SIYPAPQVSTAVVEPYN 

 Output Link: C:/Users/qiuha/OneDrive/projects/MaxHub/projects/2023-07-03-CNS-groundsquirrel 

 Correction Finished! Time:  Mon Nov 20 19:26:22 2023 

 #################################### 
 # Software Version: statTarget 2.0 + # 
 # Email: luanhm@sustech.edu.cn# 
 #################################### 

Code

fh = read.csv(file = "statTarget/shiftCor/After_shiftCor/shift_sample_cor.csv",header = TRUE, row.names = 1, stringsAsFactors = FALSE, sep = ",") %>%
        t(.) %>%
        as.data.frame()
labels_d1 <- as.matrix(fh[1,])
N_feature = nrow(fh[-1,])

# change row annotation for heatmap
fh_mod = read.csv(file = "statTarget/shiftCor/After_shiftCor/shift_sample_cor_mod_hypo.csv",header = TRUE, row.names = 1, stringsAsFactors = FALSE, sep = ",") %>%
        t(.) %>%
        as.data.frame()

feature_name = as.matrix(fh_mod[-1, "sample"]) %>%
        `rownames<-`(rownames(fh_mod)[-1]) %>%
        `colnames<-`("name") %>%
        as.data.frame() %>%
        rownames_to_column(., var = "variable")

• Features = 112

Data preview (after batch correction)

Code

#rownames(fh)[-1] == feature_name$variable
rownames(fh)[-1] = feature_name$name
# display table
fh %>% 
        #mutate(across(-variable, round, digit=2)) %>%
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

	Hypo_39	Hypo_36	Hypo_44	Hypo_25	Hypo_48	Hypo_52	Hypo_21	Hypo_20	Hypo_55	Hypo_60	Hypo_19	Hypo_42	Hypo_37	Hypo_24	Hypo_22	Hypo_43	Hypo_35	Hypo_63	Hypo_66	Hypo_54	Hypo_65	Hypo_49	Hypo_53	Hypo_23	Hypo_31	Hypo_45	Hypo_32	Hypo_57	Hypo_33	Hypo_40	Hypo_47	Hypo_58	Hypo_51	Hypo_46	Hypo_64	Hypo_59	Hypo_27	Hypo_34	Hypo_26	Hypo_61	Hypo_38	Hypo_62	Hypo_50	Hypo_56	Hypo_41
class	IBA	Torpor	March	IBA	March	August	Torpor	Torpor	August	October	Torpor	March	IBA	Torpor	Torpor	March	IBA	October	October	August	October	August	August	IBA	Torpor	March	IBA	August	Torpor	IBA	March	October	August	March	October	October	Torpor	Torpor	Torpor	October	IBA	October	August	August	March
A(+42.01)LLRGVFIVAAKR	1315.68240	655.83984	1121.12791	788.15204	1602.93819	1361.12447	1235.89674	112.12383	1545.03202	328.98302	314.99566	1791.67771	471.18133	866.97065	2517.49716	490.65384	608.49680	228.72778	346.84157	70.95035	20.36681	1965.74990	600.97101	507.07933	1270.87058	2706.28993	2628.68391	266.92906	595.07694	145.47162	4029.91145	298.17504	3064.42264	4020.88673	1415.33174	386.82505	3195.23353	2189.46752	2696.87066	252.96496	2045.23493	99.63572	1104.36199	306.71199	3456.24152
SAMLIQKL	1668.9327	363.1559	483.2648	424.2023	1011.0798	366.0579	532.2747	24.2938	1404.9710	238.4733	851.4304	1747.4778	969.4531	771.8789	1359.1032	1525.8198	2301.7407	421.3011	861.2710	413.3328	456.8520	2266.5017	835.4080	753.9010	1058.6218	231.1304	3183.7423	1171.6587	110.5091	697.6131	5197.7628	530.9353	467.0912	1903.6751	999.8112	948.9265	2123.8967	2378.0592	1430.1423	488.1696	852.8596	401.6412	1102.6395	337.7679	2237.2285
TDYLMKIL	67.435461	12.977886	4068.001054	139.552738	71.146670	214.775078	3301.186518	604.238458	194.579560	24.248800	12.021988	398.690181	37.066941	2518.692070	1079.165626	76.772633	972.479077	17.620078	148.799910	11.134950	60.757625	3720.101812	18.229590	26.176827	1455.685996	311.032799	2551.993328	41.725856	11.373961	10.154092	4453.139695	33.048519	1916.286125	3017.163028	1010.950972	3.453082	198.659192	331.678430	524.499274	3.744427	2248.493363	780.615439	804.001905	580.148269	616.618100
PYQYPAL	1741.60002	481.23119	1453.43748	11.87246	575.87294	494.60647	1216.80415	211.76872	722.65919	187.48842	426.07064	1245.45354	386.40090	1334.35924	1799.15793	415.16802	736.67991	134.91735	190.29295	224.85934	95.36949	4811.04707	508.62113	340.10326	926.06064	2518.57325	2881.37491	17.49807	364.57351	95.40546	3048.73900	169.38076	1538.96028	2562.05469	13.38581	130.22766	2070.10491	1587.68795	1760.33798	146.49821	1821.64255	42.73377	730.23727	132.49346	3688.84357
SESLFVSNHAY	2545.3557	1185.6933	101.0900	111.9813	1282.0527	342.1140	539.8326	503.4833	467.8502	447.1464	168.0687	1010.7971	1018.9807	496.5088	1028.6065	1308.8936	868.4996	357.5108	425.6689	406.8285	537.1407	1068.8689	575.5783	1255.0758	769.9374	1876.5679	915.1462	1435.4126	180.0955	620.7060	1133.1823	492.9112	495.6812	775.0884	174.3252	1546.9690	3853.3532	3337.4724	1649.9874	604.3092	525.6514	669.3254	1190.2094	800.7884	3555.9395
SLFVSNHAY	2017.54333	645.99983	467.23945	51.48780	1120.96761	483.98094	1083.91264	296.45270	759.14947	401.29325	588.08353	1342.90775	695.44720	755.05181	1393.61570	649.50259	961.31707	171.86807	286.49359	311.10778	222.80918	769.11809	719.40141	749.48708	970.13816	2178.23610	2010.34037	547.84995	57.51263	291.50488	1880.73049	228.22869	1207.19081	1020.53043	65.31173	525.22503	2606.08226	2353.83185	2268.07410	285.09653	1495.13394	217.07939	961.98255	405.22093	3904.52265
GAAAQSLYIANHAY	517.8014	817.1748	111.0039	204.9445	2997.5857	415.6172	391.2356	433.0445	246.7973	479.0652	335.4555	1655.6503	659.6131	700.4653	687.8175	1391.1158	432.4120	229.9329	1291.3965	655.8816	668.1767	1030.1975	418.5662	1964.6463	905.3349	2050.5119	783.6691	1624.0140	1736.6451	751.7404	341.3221	518.9663	386.2194	7301.9720	481.4409	1310.9308	3503.4434	2473.0730	1704.8030	621.8653	1489.5004	883.0356	1378.1436	1259.7863	5065.2790
SLYIANHAY	1870.27438	590.61307	161.01549	92.75905	1398.25253	832.44527	839.73995	279.59108	917.38352	890.88929	957.72133	1676.26395	779.46480	309.01636	1670.19826	643.05832	909.54124	206.21374	548.53370	308.69601	218.36033	598.45124	664.33889	644.30652	650.50952	1284.08458	1773.69980	522.90174	48.45130	263.58778	1597.34417	242.89404	1177.27671	972.74945	67.18362	481.17499	2420.39201	2219.57416	2013.58413	485.31142	1620.95558	197.75360	841.15173	299.40722	2602.57842
DIDTAAKFIGAGAA	184.30125	1328.05989	1054.89639	388.73821	4247.51363	631.96325	118.59678	57.02926	282.07835	1262.62119	838.49143	862.18165	1692.07872	708.53758	431.70746	1366.77675	1924.88621	597.12097	2531.12807	1201.64505	358.81252	708.63236	522.30269	769.57079	315.38326	233.91816	369.84735	918.77866	20.93615	413.09381	163.72493	572.13806	74.54679	4043.39462	911.85628	3261.93763	2303.27450	3631.96703	256.71460	4966.88295	200.44013	899.54337	1953.10518	474.37841	389.14070
VPPVQVSPLIKL	13003.38560	416.49789	532.25382	476.59119	533.23589	317.42618	271.19432	2529.75559	297.67801	505.72656	3453.11082	2054.58028	1139.69572	349.53881	1820.31988	1212.32572	68.70116	258.30758	1029.55532	290.15995	600.19710	1012.41568	167.11060	2338.56044	665.02996	2654.76407	611.91298	2739.72860	775.34768	665.50402	618.65787	546.27421	262.94218	539.90281	276.02108	600.02365	1847.36616	2962.42205	1636.17632	505.60022	1129.78968	931.19394	487.48245	686.55179	5273.25542
VPPVQVSPLIKLGRY	7389.2492	1139.4642	468.1694	137.6368	571.4592	713.1803	1226.2811	1379.3308	802.5125	539.2525	2490.4598	1890.0057	585.8936	1637.2216	3494.3400	1009.6670	429.0583	343.4559	214.8177	342.6635	265.7523	1086.8671	1128.2660	1046.6875	2342.2753	8122.4757	350.5417	655.3660	571.2623	238.9696	1465.3410	338.9685	1159.8323	1996.0955	1235.5022	396.7525	2729.5038	1334.3468	3495.4952	503.5726	565.0107	649.8454	211.4874	241.6375	1226.0691
TIDFPEFL	1806.32413	127.03844	3240.45160	180.51450	656.54251	1045.12973	3050.74514	771.66613	1474.68880	419.02958	108.76937	1081.84161	438.12802	3048.72702	1912.68892	37.03243	937.24414	4101.92972	227.57787	237.01734	21.92182	10586.44080	2084.90365	134.52667	1471.50476	1475.20839	7515.67175	416.39432	307.75033	133.31933	4634.14622	68.18823	5725.30052	3202.29651	108.20187	145.50248	937.74510	1386.85930	1511.12552	150.89469	3310.80532	25.65043	2625.48759	10.56005	7237.96871
Q(-17.03)EDAELQP	829.93528	893.78247	68.50192	2576.98660	518.74072	478.86528	124.92619	942.50111	139.89478	1015.78750	25.48683	21.40669	2042.19337	334.02023	467.04846	2010.35752	434.89938	1951.66368	399.75780	1121.88435	8991.40588	53.50582	66.46285	1977.27951	327.40081	104.56667	61.45111	4493.36324	2547.17302	2763.49845	68.50686	6876.27067	96.62173	49.96099	9719.97137	14947.53745	259.99439	315.24267	321.00068	4733.52257	30.39904	2800.86090	177.24814	1753.54788	121.77835
Q(-17.03)EDAELQPR	550.490707	404.281428	382.768143	1431.834990	415.328069	126.566055	141.463794	573.048696	152.284817	565.618645	73.253103	363.117238	1049.832807	145.676824	107.643002	662.861605	392.596653	1533.890421	201.594565	992.818889	3523.626831	418.215292	279.094263	759.515372	149.589024	59.434756	233.388045	2648.987837	1524.906493	1017.367660	488.908727	4095.500228	4.732894	29.606924	6654.384546	7988.393161	448.313791	302.571175	140.137131	5442.426069	524.106753	2463.850653	718.045969	1435.198012	1149.312867
SAVISLEGKPL	2376.52556	883.96065	43.91354	107.34422	1629.16546	567.28066	411.67608	265.73648	530.28420	894.05205	396.12946	1368.58125	1062.40819	480.68616	631.20462	1310.75029	713.70855	388.47299	543.81682	430.13431	822.71403	814.27694	490.94228	1586.16861	364.76088	2141.76108	1353.93474	2112.67545	227.11485	581.95827	1320.94215	486.16729	329.44057	1124.65742	123.72279	1331.98842	3798.47207	3051.69871	1211.15411	899.17102	380.85223	1070.40097	1282.02111	708.08699	4525.52145
FLGEAYHHVPESQ	1184.385255	371.623145	313.801916	1832.243514	1541.101239	31.003088	143.132113	719.946817	9.951043	406.923822	264.150801	10.851258	1590.273379	239.505447	497.042221	1027.356515	587.470044	734.190892	560.083335	528.973689	4652.163000	747.837862	18.881968	2005.656372	714.074324	342.229506	645.443204	4683.779598	6102.048181	4440.448225	1335.323326	8094.810358	431.980488	688.424461	5457.750771	4819.834380	1991.417446	1488.111293	1302.889802	5334.029769	1207.346854	969.784803	513.571891	1484.001833	1484.833432
FLGEAYHHVPESQRD	883.103665	466.577346	318.349484	1851.480381	1546.601640	109.562605	143.451399	769.467476	31.899257	458.808421	310.590962	117.919239	2002.028117	191.402712	254.663596	2193.136254	403.520290	893.974956	165.768611	899.590329	2680.680821	373.126297	174.699304	2528.846808	196.040759	391.243579	201.505794	2920.321486	3232.402137	2734.800617	5.916908	3639.612065	38.971922	5.768712	4078.877576	3183.437213	1241.576635	567.607463	367.568698	4498.119463	521.253804	986.459701	385.054757	645.767888	117.830586
LGVLFNPYYDPLQWKSSRFE	2120.0408	561.7486	216.3327	3177.7105	2483.1042	467.8483	550.4244	3507.8755	760.3000	1272.5528	333.5300	159.0327	3305.1724	384.2099	603.1651	2776.0209	1117.2108	2086.0901	902.6061	3914.4681	3939.6927	129.2200	961.1741	6072.2363	972.0429	583.6718	311.8980	7343.9641	4425.1941	4503.2004	652.5093	3806.7880	260.7798	220.5818	4155.4763	2797.2877	917.0212	928.2957	722.4769	1807.3196	476.4778	901.2828	706.3177	1966.3022	165.5905
Q(-17.03)YDRVAELDQLLHY	2301.7919	856.4154	115.0936	4781.7563	2736.3124	679.0251	480.7813	3143.6741	545.0804	1317.3332	253.0503	298.3487	3515.2760	479.7156	382.6381	3845.0459	789.6765	2982.8019	1063.8123	5080.4857	3556.5246	452.6325	1155.8874	7759.6287	774.6475	626.2487	690.7920	12925.3332	5427.2161	2641.3555	782.0290	4167.9204	393.6126	575.0020	3556.8673	4207.6182	1246.0449	1212.0580	781.9702	4204.2092	437.3828	1325.2453	1343.4904	2069.5529	977.0923
SVLISLKQAPLVH	2853.9143	629.6019	497.2525	527.5814	1155.3535	225.4971	403.3678	266.4400	1467.4787	1119.7356	455.8151	1189.7563	463.1049	1181.2760	1712.4103	822.0466	331.7738	1498.1772	283.6045	1476.1933	209.4044	1450.9245	858.9922	1163.3815	814.4855	3285.2910	2240.0147	1629.6937	1044.5775	868.3403	2333.3997	556.3949	876.0992	1068.0507	772.3092	454.6820	1272.0640	2701.6685	1994.0305	126.5815	1386.2519	668.8278	346.8887	567.7428	3859.3534
TTMIIDHVVPEPG	657.28904	177.85053	4084.58006	421.17146	563.85102	629.81309	2036.07395	902.41043	661.09599	1040.68262	39.43688	404.67377	866.61882	1835.93794	813.35022	629.37638	2291.43950	2004.05671	1515.73649	11.97264	1895.20895	1198.28302	659.32373	379.05818	99.68317	1424.37340	2240.40517	144.22998	689.28785	376.19727	2686.70186	230.70446	1222.15030	794.93581	983.32864	85.97098	1905.65238	2497.34720	1041.67467	363.31980	65.50756	163.29992	2611.73168	204.44337	4243.06357
TVVYGEPITA	615.126494	106.934585	1216.591820	6.446893	369.418331	307.821072	845.296103	630.553114	232.491235	86.460757	44.089549	434.304882	321.259402	1621.733572	1118.356568	241.314899	2886.282079	56.059461	455.006533	28.980890	16.158049	1816.838091	1153.937862	133.519931	842.547381	1603.638237	2083.931665	6.231272	547.515168	9.719374	2172.142692	12.905570	558.881758	2806.282165	28.962698	39.038401	567.318761	302.251012	372.470614	92.078878	794.463795	4.244443	672.385339	7.268217	2566.251216
S(+42.01)ILKIHAREIFD	1740.0115	1046.3772	1130.0911	48.0409	2629.0375	1827.9920	1238.1216	336.4308	624.3364	878.0637	547.1298	2538.6262	994.6428	1708.1572	2971.7012	1732.0048	2623.9554	790.2740	1189.7865	762.3408	292.5069	320.8429	1226.6997	1899.1594	1734.5414	3228.8996	1142.5909	893.3286	249.1331	1059.9523	3257.0049	479.1520	1116.6592	4091.2621	204.3385	551.0258	3068.7630	1397.0887	3072.1397	1055.8264	1396.3427	519.5071	816.5776	433.9328	820.1476
VKVGVNGFG	1550.18801	2276.35456	1542.39365	43.55158	3386.28548	779.99510	542.08314	1021.93710	657.70845	1149.09095	337.01592	2065.89928	1509.71694	63.13213	1432.24129	2082.90228	171.84585	642.79217	707.22451	473.26260	525.32477	2025.65865	568.18328	1607.55129	52.96214	405.94865	389.82085	2215.41045	362.28456	1008.58925	357.76450	874.32371	507.18712	512.93846	658.95736	1818.29134	2701.43074	2478.33296	756.23500	1226.39638	560.20993	954.73726	1357.20057	1023.35681	3952.34684
VKVGVNGFGR	855.8731	1079.5823	520.6358	606.8479	1628.8440	552.8113	1088.7209	407.1985	1497.2078	837.7228	1191.2021	2089.3398	782.3706	1602.0170	2522.1914	1075.9823	1734.8781	864.5905	368.8310	775.5858	937.1450	752.5723	820.3911	2242.8827	1222.8261	2598.4098	741.1805	3096.0501	525.2268	1275.8316	1361.4497	1522.3545	1833.7710	739.4245	890.4898	3206.5500	2507.2262	6526.5058	2163.9931	2932.3072	1852.2239	421.3947	1646.4742	631.6286	2169.2971
VKVGVNGFGRIG	1186.39134	2283.98833	598.25391	89.04525	4805.40313	1099.18567	609.16694	674.17139	764.09567	1533.20582	413.96922	1047.26515	2128.25565	637.59755	318.92559	2737.19440	701.89311	879.66689	897.09287	564.11935	1118.97296	371.42126	661.43755	2056.85826	592.73700	138.67631	99.98044	2774.11566	405.43055	1452.62864	291.35999	876.36649	407.04229	707.23533	656.27515	1935.84461	2477.84799	2467.51206	896.79784	1467.56305	387.20737	1172.73081	1507.50437	1308.75998	4053.83013
SGSAKVAFSAIRSTNH	1843.385501	188.758802	14.302507	1774.619558	1219.737335	376.791594	205.132539	1260.031000	402.181127	337.658154	556.253008	548.899476	1378.395916	205.089997	6.673509	2255.247208	134.781575	1261.269773	206.532073	651.706972	2278.829343	546.426707	481.074247	2286.290926	33.580157	38.121339	334.499709	1661.548837	1904.569792	2033.479576	722.953813	3515.479629	367.259856	437.522545	2958.034138	4474.721945	1219.309739	254.458590	471.580417	2147.162103	473.654465	1200.846302	11.155718	1042.155962	696.553270
A(+42.01)GQAFRKFLPLFDRVLVER	5939.5473	491.7480	660.8219	648.8974	542.9012	1907.6274	1663.4835	2300.2986	1022.1315	473.2915	1039.2812	1749.5892	1388.8225	1791.9053	1340.7088	1271.9964	1807.5474	353.5517	845.5340	563.7801	1032.5646	954.0117	996.8144	566.2500	1918.3044	4697.2837	1516.6250	700.6201	805.2720	169.4016	1860.8843	732.0176	1323.8725	2293.1081	1088.1412	205.4172	2368.2805	2586.9612	1825.7324	877.9538	1021.5198	130.6356	2747.1930	287.4780	2209.8528
DILGKYVD	27688.1857	2744.9728	902.2681	1607.8352	2121.1430	1228.0457	543.0431	3127.7877	451.6974	689.4905	929.2235	3833.8429	2338.9091	676.2794	202.3431	2117.9054	2823.6691	308.9513	831.5667	552.2165	1340.3345	2382.7778	1783.1123	4844.6002	2785.6320	6456.1890	1789.6489	5242.4076	1497.4195	177.5460	635.5564	1057.0180	935.3865	1522.0489	649.8517	2369.9898	5730.3147	7429.8847	2282.9387	509.7049	250.0608	1489.6676	2192.4636	814.7411	6990.0337
AEALERMFL	1178.330472	225.347950	927.642801	192.375854	61.756329	108.451388	552.466214	141.001382	623.208934	47.559465	477.368316	6638.189381	182.088381	3.838443	1592.237446	74.355965	477.428404	1630.047987	90.915891	31.688602	1.874399	1409.589820	283.919788	91.323993	516.659499	1399.549649	1877.417821	234.167871	440.711639	29.483886	1315.414170	9.798131	748.517398	1482.785465	453.959894	18.590391	524.574949	1580.220584	2653.359464	296.313244	2971.098120	772.117828	1112.376176	138.254038	4395.016486
GAEALERMFL	1103.462443	269.823470	1232.016478	43.511580	99.915834	293.957867	216.324116	293.603637	1263.988541	636.076246	513.486128	6385.703684	247.062268	613.671394	1961.928828	22.176429	182.261883	2231.479012	36.521104	74.407597	483.117008	7409.626477	468.576665	71.459894	636.247438	3467.602430	2403.572466	166.123446	1.676591	57.766775	1518.038528	13.831946	1099.497196	953.352316	22.117807	78.330217	545.977438	1416.093799	2839.176250	36.940433	2644.712991	30.668116	1001.849250	55.903422	2953.065164
PVNFKLL	787.47963	112.85291	588.68319	39.61983	60.57051	98.23116	358.01268	297.32683	831.69431	44.29408	728.61692	3013.84751	329.27648	867.79654	2935.84371	71.27384	72.36624	16.51919	55.80963	86.46703	12.03821	14342.54676	192.25844	83.70033	923.71923	4552.98264	546.78643	87.03537	376.93662	112.38145	2522.05449	33.56718	2088.57129	952.62070	590.11581	35.55677	756.66509	499.26589	1326.94013	269.45834	2184.44493	14.56621	60.46611	51.78147	636.04822
SLDKFLA	1339.2631469	55.0427912	417.3694924	18.0306087	87.1911168	158.9971520	392.4692964	34.2973416	898.6818104	121.4705428	701.9898865	6382.2810242	617.1214788	391.0818441	1926.5274336	117.1452985	405.1363899	16.7094129	60.9147116	26.9694921	6.7107549	3856.6229491	469.3287509	12.9244410	761.0329029	1793.0711372	2314.7410750	48.4799491	6.1100191	95.7947589	1320.1660644	40.0009767	779.2782522	393.8665895	0.9652866	19.9460273	306.8804326	762.9719267	2181.4669154	26.0119334	2931.6276657	21.8475471	492.6295850	39.5159504	2582.0133439
SLDKFLASVSTVLTSKYR	1435.81562	3233.97430	81.82640	960.35609	1838.25093	709.25885	19.88857	5678.75925	393.35938	167.11263	322.84528	10507.67986	564.85883	241.26526	528.87916	1129.39611	47.14948	650.87573	190.43287	796.28516	89.25659	856.71317	145.90811	5257.69851	201.49069	821.73029	61.27346	5021.65571	651.91577	1659.37970	174.33019	161.58045	557.82947	493.49282	72.80873	1654.58468	6837.68479	6234.37829	2544.84460	47.18579	1269.93206	993.54913	3045.66898	2112.33590	3488.48098
SVSTVLTSKYR	1027.05638	1346.94256	144.75392	153.24640	1581.24969	387.74074	152.40063	2801.58303	291.73135	533.03080	423.99420	11025.02622	480.05166	14.46321	229.62020	555.89052	122.86271	171.12369	85.22064	251.86349	164.55800	79.04946	183.63797	1611.64864	194.24658	2404.25356	175.77000	2039.33619	282.47836	786.49223	928.69417	327.55862	738.68112	341.50298	114.82097	2077.92737	5183.82544	1450.34318	496.19972	330.23584	773.34141	456.90378	649.22997	966.84423	100.00852
TPAVHASLDKFLA	1896.262586	152.339360	23.264942	193.582866	58.758042	213.667533	253.800055	182.968217	250.338250	106.213763	677.196058	10646.733694	387.968618	551.804405	3013.552014	165.233070	354.471425	2578.765197	115.153609	37.578656	413.141950	2087.364908	456.482804	138.148745	766.105422	5289.336480	1418.941542	106.146221	1.960773	135.019234	1125.057037	20.814082	338.184899	1488.033317	423.429257	3.859485	1675.301773	2467.499852	5532.525575	33.329057	3249.816790	2202.862829	2480.765074	240.612539	12102.712027
TPAVHASLDKFLASVSTVLTSKYR	1707.90700	5067.24523	343.62382	1758.38374	1498.20363	547.31608	200.84503	6663.67556	357.16600	1312.49816	388.86625	11797.99482	348.80770	86.76362	663.92503	601.37795	63.58443	206.91315	693.90634	550.72425	130.62876	669.44311	477.54167	4546.79185	151.92628	518.23147	340.85791	2452.51991	271.35084	266.15279	581.14722	198.09244	529.45284	119.81690	788.54501	613.17353	6069.23020	4271.51901	1075.41252	864.28857	327.66855	190.78222	1169.59059	994.08066	2744.02549
TYFPHFDL	624.617895	22.299395	688.588625	44.024523	23.737081	93.313543	434.344891	44.687792	856.467572	48.584295	347.960452	4120.737160	124.655782	639.726444	2402.728551	14.774809	144.977726	2016.542174	28.893194	25.971647	1.166269	6776.943419	289.797167	26.742224	624.261530	1285.165781	2510.299228	15.520166	262.555208	38.529264	1799.111370	34.557507	1788.445826	618.095623	426.009518	5.009722	161.162658	587.264901	2790.051969	4.571831	5183.379632	2.065370	344.606349	4.958326	1707.323606
TYFPHFDLSHG	2743.33377	215.62126	209.09161	40.19449	298.84711	248.66102	280.52417	153.04584	819.42098	131.78958	778.32069	19581.89126	553.61710	416.83646	2581.05422	122.96975	101.28908	23.75846	99.26237	61.36285	287.13269	1416.06137	475.38668	168.69078	81.61208	4489.15248	1448.58128	93.87148	675.79984	30.58247	1020.31495	201.04457	1169.33244	1329.90311	581.84733	115.95382	890.74796	2665.75493	8932.44198	59.72874	7233.81490	670.93478	1048.35006	50.31616	8078.71959
THYKLVPHQFAH	5565.52060	276.46488	168.95016	129.72093	560.62676	884.24901	951.23644	630.73707	1294.13827	415.40234	2271.19555	1701.58540	855.97130	649.78534	1703.11773	956.60331	697.47999	363.89356	666.81598	467.91752	195.68055	760.82193	998.64609	1066.40863	660.86401	5455.72380	1221.56270	467.39739	171.96340	437.23859	339.33323	413.99980	571.98303	264.86608	23.87475	290.02629	2605.53501	2125.14095	1926.68679	528.97183	1364.02011	305.67948	1095.89411	331.16370	3604.45873
TAYAIYELAKA	2411.008142	738.850409	548.222341	347.464003	119.419344	420.510002	1001.525909	171.899081	1401.579138	336.992204	775.724887	3409.507900	989.512512	1125.162035	2332.279654	398.093671	1478.639090	119.157939	117.803343	205.494359	108.046366	1630.153223	1066.375794	174.460811	1434.909274	2140.043232	1707.606964	61.237609	551.537571	36.312336	2568.778927	251.926877	1037.718566	4382.067609	1232.125405	2.941007	1419.165056	1534.687992	4218.374668	1108.752576	2729.799921	18.709968	846.157607	688.991758	3746.974920
TAYAIYELAKASFPKKQD	2007.7505	501.1635	470.4856	524.9842	413.2176	790.2663	513.7141	934.0451	657.4523	676.8837	658.9325	1871.1860	2306.5039	524.9254	125.7059	1584.5145	425.7228	2305.0878	750.8259	1603.5388	369.2813	1509.3800	897.8889	4653.9980	1017.1826	4541.0270	768.0360	1424.9538	292.6139	1692.0285	1781.4691	240.4045	645.7246	895.7017	1385.5762	867.1989	11009.9536	4040.8321	2086.7463	1243.2823	151.9777	637.8876	1510.2070	1085.5501	5781.2413
SGFAAPFFIVRHQLLKK	3067.40898	465.57156	1576.74765	304.27005	3970.87763	2785.09076	76.89665	739.43543	2217.31054	474.88540	206.43749	1941.88785	1713.91919	787.25622	2011.74225	1426.89301	361.23842	713.61161	136.68111	703.47614	547.43367	790.26968	623.59561	891.79261	1431.29022	7183.84468	540.29373	121.42776	92.91465	929.05661	1581.51102	230.01590	1733.32496	1730.45058	1074.13935	637.07101	5561.03649	112.42796	5776.51101	293.51275	546.74844	1035.47885	292.64579	965.92645	659.31347
AFQKVVAGVANALSHKYH	1816.21675	2074.04044	411.74022	272.92404	1525.00119	236.32202	226.26463	843.97532	407.83234	265.39188	397.23558	9499.09267	388.23816	259.52948	56.04023	1246.47685	520.30696	2494.30608	862.48102	1285.91314	405.98469	986.81198	465.46847	2528.29852	567.87183	1875.61761	343.12721	3485.38759	299.76187	94.28183	1217.67959	44.05874	588.74232	992.89282	104.71627	1886.19912	2295.97211	3234.14066	3666.21086	33.28464	1045.86791	575.05528	112.21810	784.10468	2076.46260
KVVAGVANALSHKYH	2243.90169	3991.70027	373.41222	530.29289	2432.77893	671.19478	316.82046	2214.65939	454.42969	38.51508	335.42882	9825.49696	557.72429	167.94261	832.39148	1602.35080	569.91564	298.76455	360.86941	417.35609	210.78870	903.40935	435.82817	1735.92144	402.19707	1695.52102	501.11833	2149.46272	277.55751	828.72553	140.91840	398.41511	517.45278	184.46869	19.38739	2008.62837	3673.96297	4093.72098	5008.20522	358.77505	934.69184	630.35474	1142.14337	910.00827	264.15537
TPEAQAAFQKVVAGVANALSHKYH	1652.75485	2056.22894	215.17131	126.82713	864.88395	489.99676	132.90983	1210.12517	861.06141	223.65900	262.36296	7593.32303	539.29741	515.76576	1286.48176	518.63183	306.13337	319.00022	264.92900	342.12126	94.28212	290.17960	157.76149	1067.39714	425.38780	2683.34421	724.76491	1416.99851	143.80581	541.13968	419.77203	188.32943	147.39599	970.29651	31.69467	566.40827	4573.22975	4948.34959	6592.79326	118.35293	1207.74009	437.73695	3284.07478	821.38348	2826.05801
RTLYGFGG	2673.23384	1412.29582	514.65715	523.84880	2511.30318	635.80288	434.39649	1497.82733	503.24158	273.22841	391.96554	1677.32042	1150.70609	99.60693	576.32682	1447.95762	379.12818	334.45283	249.88105	413.25588	903.87317	714.33406	229.56885	1822.76461	354.70970	1253.11304	299.54683	2050.26137	255.52635	845.24690	464.03051	712.10099	535.04797	564.67902	1034.03045	3343.08226	4254.88937	4282.50601	1225.47236	1071.87889	926.87714	1144.57815	762.44741	1279.09034	5330.90363
TLYGFGG	2266.36221	404.96948	563.33995	589.87906	435.57869	611.68276	896.64372	510.56076	616.59670	294.84533	509.25588	1185.16009	344.67045	1501.03218	1150.47458	587.86696	765.95262	138.09224	317.90250	66.48264	770.52232	3244.04510	564.47598	648.19267	688.92378	1505.93464	2000.90822	1020.64732	224.23599	344.91709	4432.66942	245.51784	1632.48819	718.42322	358.13775	378.68501	2066.65472	2204.23180	1822.31681	593.97520	1992.94186	213.73968	778.69932	366.58023	2697.10650
TLSKIFKLGGKDSRSGSPMARR	3398.3320	916.3653	620.4603	1029.3850	778.2236	408.6576	429.7236	387.4170	367.9496	718.9060	385.6085	7749.3563	436.2870	499.6988	569.3494	928.9858	1119.5660	205.7834	967.6515	949.9550	137.5194	3300.7890	549.4336	3596.4393	701.8602	9093.0495	1142.4891	2082.2478	353.2823	1617.6696	1729.9478	144.6616	708.8183	1055.5131	1154.6810	393.9443	8582.6276	4967.7809	2503.8655	1558.6692	1811.3318	247.7774	165.9128	1035.5488	7542.7417
SIGRFFG	3053.527414	52.843620	737.528380	29.292068	82.398252	87.634216	910.933219	84.914067	302.487278	54.084796	1919.458123	3006.221408	145.181300	241.504640	3485.040415	210.694638	389.977073	14.326104	49.783623	105.451676	511.206002	5948.366580	491.284512	106.985442	817.562964	7402.963375	1299.301585	126.110023	9.425425	32.083130	1311.732260	12.878724	765.758388	527.037832	257.267701	11.837019	362.186536	655.724222	1058.686912	7.887293	1225.357519	750.101638	146.728883	1.840266	8220.604523
SIGRFFGG	3160.000405	36.263083	668.762447	28.832578	17.358438	149.814095	593.229459	90.171792	109.424556	13.518884	1358.244103	2787.827905	145.023572	267.384552	2560.588658	134.885023	170.001567	7.129067	7.382734	19.158083	12.748518	3895.829279	445.295704	93.365039	672.920739	7858.627672	725.189130	90.028279	451.175891	41.238168	1543.056522	70.639045	854.992379	209.440947	3.793858	6.001923	358.461044	678.636742	752.103749	1.078285	1565.770153	1048.476271	79.512638	58.854859	11156.433880
SIGRFFGGDRG	4584.90434	110.88568	500.56191	365.83208	63.44133	276.59575	758.11731	237.10125	723.34632	164.33271	5691.75468	4268.81601	826.75655	567.83537	1819.66525	477.85587	691.15656	61.49507	163.65575	908.30117	177.64990	1131.85434	935.20923	213.37343	1038.30301	2051.18963	210.48651	190.10562	525.88909	66.51984	784.31331	213.01215	265.98426	638.55643	197.89607	13.48851	346.33693	800.22937	1642.65836	77.12604	718.06631	38.40883	176.64415	184.00163	745.28426
PMFVVNTNVPRA	1948.63083	767.77372	292.69394	11.48820	2024.72223	717.47731	550.80510	261.40638	739.25921	892.57029	179.18092	598.49856	966.66172	260.99038	821.08533	1354.37412	1274.58540	197.87932	301.13589	538.23700	507.83423	168.95368	468.02225	1738.38686	1604.00605	2040.62287	1677.37453	1904.61203	10.23634	620.66589	1518.63302	723.39732	665.54119	3042.06787	1361.33311	1635.25127	5568.13493	4996.45833	2420.10576	1089.04145	1190.98927	840.64061	1764.48224	711.51488	3634.47630
SSPETLISDLLMRESTENVPRTRLEDPSMW	143.1640	430.3827	696.2983	1168.6956	3915.1731	561.8927	780.0263	1534.1005	565.8407	1575.6212	630.2778	692.7094	2406.4080	53.9575	411.6411	5378.1506	1617.5715	14629.2947	4273.4529	3363.5340	3420.3068	181.4642	406.1901	9437.6176	802.1310	617.2038	899.2631	3208.3466	1791.3869	535.9394	736.1207	4709.6586	649.9062	581.1618	6462.8381	3511.5576	665.7996	1172.3576	1126.2870	2849.5717	920.6387	986.3500	1058.3524	598.9404	773.1287
YPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY(-.98)	664.16483	258.16425	430.87092	1035.19858	1072.74311	102.12846	258.80976	847.32689	190.04662	440.59213	238.57165	369.45745	932.82577	59.53859	281.65679	2000.41125	350.08779	10259.50586	1593.55584	1003.40603	4072.34217	588.38858	58.23029	2591.64038	222.62700	492.39451	285.11719	360.92187	1686.42164	3391.72601	747.71984	2939.56412	15.29948	655.08583	5344.75633	6342.65296	1072.66108	535.60247	306.24346	6675.83133	105.65504	5520.95226	365.75599	1913.53983	198.81864
AADQDLGPEAPPEGVLGA	1606.07294	722.01543	288.98836	1936.37740	1141.73929	349.47386	76.74345	1052.09620	539.27687	744.87170	538.08092	127.66776	2402.43611	67.79459	156.15815	2075.77845	893.21590	1542.43709	201.19751	1369.49796	6694.08611	270.21975	332.37067	2142.11330	425.74206	592.40016	26.64746	4264.36988	2869.41617	3028.09871	17.13207	4298.60943	35.01751	111.93269	3934.10790	7379.91932	823.80864	817.20422	298.22514	3207.79416	20.17141	1926.71717	563.45660	1661.20825	546.93728
AADQDLGPEAPPEGVLGAL	2439.03226	160.84264	111.65962	3092.22269	3823.59308	1080.37657	67.98434	3533.67637	12.92714	1141.50920	376.78211	1006.96672	2104.68373	297.31882	342.24546	7412.90075	2115.28432	3570.20292	734.35473	4103.86684	6347.21550	844.04097	125.70674	5610.77802	1835.55494	1446.58497	73.14011	6860.07397	2924.22375	776.18119	893.56822	5726.66878	60.59772	267.56836	4493.49117	5914.09879	1693.21582	987.46493	560.26961	3410.96645	888.28493	2496.18978	105.84658	1787.21616	1773.48794
AADQDLGPEAPPEGVLGALL	1336.806293	456.642488	81.934142	2376.785293	2265.944818	776.498215	49.233025	2558.503948	425.021164	1761.222973	186.253861	99.095125	914.172698	312.792661	2.536455	1001.823096	503.257679	3430.934528	940.503858	2701.246136	2628.175381	95.365129	950.597963	3812.839593	281.038145	242.210719	301.889963	10430.381488	3834.883409	4229.494006	37.621474	3684.256279	373.416379	7.545764	2773.384755	4534.890840	894.118094	732.488944	229.647046	3795.174707	191.313047	2770.472901	1826.554991	3537.509310	749.819031
AADQDLGPEAPPEGVLGALLRV	1422.150139	358.124439	2.349741	2839.379929	2391.633848	744.566826	251.582579	3394.902960	513.948384	1267.369080	95.498331	68.665830	2589.005687	195.334986	240.440928	3131.009161	785.409432	4385.008429	840.726665	4076.100483	3925.060686	44.075724	904.695409	5197.064077	602.744274	515.414047	196.513898	8848.379559	3911.651715	3797.973825	382.890471	4604.006336	330.822865	257.396047	3892.105402	3428.047350	730.917753	541.038338	107.845688	3819.202666	20.020109	1999.721155	1417.581487	2006.782740	505.827348
LENPQPQAPA	1425.518215	450.904187	33.357040	1188.782118	1056.007049	330.108714	25.377633	1445.184049	262.374958	570.359752	348.532370	180.181380	1443.455115	176.674471	30.924334	2088.536806	672.940244	1247.028652	274.464440	814.354789	1760.340317	7.366773	272.855597	1231.054077	320.816780	688.560625	260.911639	3300.635499	2182.253823	2184.916878	131.877556	4239.891274	2.708095	40.300789	4166.177776	6922.312755	925.093005	835.014153	513.604655	5335.946527	129.260738	2184.499477	331.962536	2189.938601	438.487319
LENPQPQAPARRLLPP	1923.602878	514.693371	260.979576	2804.729788	1849.638513	277.477900	37.231736	1363.627453	165.818764	871.428198	482.762963	87.479174	3512.664811	10.569543	229.561386	3178.728044	278.439759	1136.190261	372.123168	1066.762877	6609.853045	4.965468	157.611555	2398.242437	168.667770	382.229863	41.456201	3702.225985	2441.759218	2843.029042	543.244009	3432.605345	314.748599	381.882289	2507.645027	4626.464410	716.030180	818.778047	291.783853	2970.456152	17.861863	1367.277261	385.101357	1676.592319	444.134714
SLSAASPPMTEAGTPRRF	1083.97568	527.14894	353.52371	1868.89867	2115.16085	212.04432	205.11577	932.05141	592.23402	1379.20450	184.94027	149.26666	3329.64577	214.80556	213.13134	3055.01209	322.47121	1513.76402	394.21429	1093.95304	8887.16655	568.97630	162.65459	2546.86716	133.95019	668.52575	287.43274	3134.11131	2854.75448	3319.04858	897.46088	4544.59495	393.45061	513.62556	3791.61993	5965.27241	548.95895	414.33848	219.24328	2499.46110	26.34713	1424.19305	412.51255	2056.60607	409.30790
SPEPEAAAAVPRRL	2207.72981	1061.83849	191.18512	140.92507	1667.58411	389.41320	225.06934	1129.87088	547.58282	1778.39011	7.85415	270.65014	1546.40358	248.55178	224.30108	1617.78707	167.08784	808.20285	1003.80573	1214.80370	2154.31269	1066.63553	817.70320	1704.74496	275.31750	2931.05706	787.59192	2529.95418	271.09332	1483.36284	1105.26267	2173.26283	86.45014	987.05414	298.38587	3352.72457	868.33015	1943.74298	376.21735	1608.71931	599.09915	5197.18188	5451.68259	3812.94635	7930.78235
SVPRGEAAGAVQELARALAHLLEAERQE	1603.73746	189.03000	116.69179	2180.98270	2929.66756	807.28141	436.41672	1816.65244	291.48027	1303.87537	314.72834	64.40556	619.32972	182.67458	326.16260	631.39074	598.45033	1875.57353	690.81176	1485.50959	2243.22443	49.39498	805.41712	1305.57287	323.38063	210.83161	207.08269	5967.12818	2184.17103	2919.32162	765.11101	998.04997	61.21350	808.04825	3543.34447	4225.43286	1024.82448	725.25626	591.54807	2869.22136	264.35418	2014.59688	554.01055	2456.00418	859.93387
VKMALQQEGFD	1433.12599	390.46610	61.93327	1256.51892	1482.61680	394.71830	34.09951	581.26759	444.39348	641.60936	428.45673	336.97905	1292.56968	309.88806	511.82880	1714.30593	562.99384	629.76325	160.91677	415.65017	3518.92091	881.49712	190.26759	1289.52975	593.50675	392.41340	375.43284	2255.56148	1712.56871	1560.72605	233.45345	2294.25190	458.79079	529.47746	2271.80227	3070.14109	800.99388	804.71241	682.69419	1867.57192	368.94549	939.32430	566.61021	924.75372	830.58243
YGGFLRKYP	1891.952767	852.948153	276.333475	2605.104810	3502.298519	315.490831	104.243092	2421.150075	138.611140	1941.996961	689.641932	49.302407	2175.522585	38.038664	240.786204	4581.127912	184.595024	1567.814369	923.132179	882.303003	5504.276328	423.207349	65.453393	4501.109351	231.625770	97.518267	196.419447	6249.794615	4086.278714	3308.880843	27.427535	5400.948655	340.038159	8.022263	4738.659140	8378.821850	814.890358	793.822935	267.058428	4049.498735	379.687578	2024.244542	477.830126	1756.584253	578.225499
YGGFLRKYPK	3212.85450	732.02140	456.84821	2812.71066	1568.53994	219.74172	308.73851	990.09208	472.74288	423.88099	577.97278	25.71017	1453.71035	136.64789	546.94455	1625.67555	541.41678	1418.76207	281.40554	626.93826	2306.35668	473.35958	377.07366	2192.98558	133.26563	736.14402	40.43439	2953.77643	2465.38627	1631.30518	431.79719	3235.62824	49.67634	347.51319	3242.28437	4692.79459	1076.93522	494.75634	865.32631	3576.96788	65.42616	1366.03673	337.96596	876.43724	580.47497
GGFMRGL	1455.387545	506.857832	183.484490	8069.431645	1792.688483	58.539591	128.359942	1359.178153	223.423943	15.264511	751.011883	744.247314	4924.914867	99.413106	409.735613	4031.578659	5.516974	882.451448	57.850210	1447.013749	8081.396316	718.317478	415.978204	3031.041676	322.011755	839.674996	249.096535	7646.190146	2484.582653	3657.857795	18.497448	934.956520	144.623315	510.201784	2800.640632	764.223707	675.603108	247.922686	768.143085	716.453948	694.647282	229.402729	527.973520	3214.888996	1179.299953
LEDEAKELQ	5542.681347	1750.431227	316.295615	6919.432428	649.544582	22.684781	548.786623	2373.356882	297.944529	7.760691	697.790523	514.658087	1974.373126	63.768728	484.159061	1998.140384	382.347179	262.625707	65.144752	592.724256	611.554072	257.769256	247.182435	1622.934832	199.631631	748.832298	97.346099	3614.031110	3714.221466	2120.797701	572.198428	566.701704	48.399845	140.616800	891.771056	2190.740318	1168.437638	288.320866	843.337310	1470.072248	122.155253	179.699067	425.713067	1483.337458	51.850892
MDELYPVEPEEEANGGEVL	1477.80414	852.23267	333.63064	5216.46462	1216.66112	356.56048	19.66969	684.41814	478.00701	1704.25107	92.78674	730.46900	4147.08863	327.84097	619.19187	3609.41823	467.17890	2512.01151	490.11313	2736.98061	4074.57505	489.98222	768.94545	6418.94364	14.82368	6.81427	249.33445	14749.74556	7608.62710	9642.74545	677.98091	5749.87874	506.42169	638.97974	5336.08061	14363.02012	783.16128	1293.22275	208.87670	2915.31090	636.11058	10346.95830	1224.06531	3091.35642	614.07945
MDELYPVEPEEEANGGEVLA	1464.41346	612.51466	207.94980	11498.06535	753.98707	561.86749	157.81029	1333.83060	650.70417	1627.23067	12.67096	927.46475	5701.17139	91.49559	10.30471	4410.36306	81.15034	2413.21107	206.75648	1578.61919	4478.30262	714.58626	713.52264	4904.98999	201.64577	781.07928	400.31531	11415.41296	4509.89797	5663.07065	45.77525	3646.43861	306.52462	41.82796	2557.39936	7313.29943	534.97035	685.54541	594.38320	1490.45515	593.28319	9774.93078	78.79367	2768.70527	513.96156
SPQLEDEAKEL	905.38078	433.14202	362.04470	812.45346	1942.66274	259.96174	127.16736	635.16852	275.38577	758.77396	53.98866	610.45281	1140.62650	130.63252	119.06724	1931.89870	389.49505	575.92854	634.75379	936.27799	3115.99187	387.44283	47.00117	1181.94548	190.90042	7.16430	245.29294	2945.47721	1433.55962	2156.65064	64.66140	2313.46556	165.66872	105.37535	2114.42766	6096.71677	591.05524	796.65628	507.76140	1669.41057	449.61119	2027.46857	635.02868	1021.36591	537.76417
SPQLEDEAKELQ	758.742870	576.444881	253.565995	2855.290937	1206.858532	341.776479	328.261123	1019.267292	122.807560	874.810311	126.410214	24.740385	2145.887447	32.209812	408.788777	2486.060214	42.977046	792.295117	185.792055	762.944943	4142.037894	22.732269	94.246356	2494.380346	393.884279	18.430824	202.001162	4672.677268	3331.901214	3332.647052	20.039360	3500.636173	376.831253	586.373544	3373.070721	6437.953242	365.701302	1.937352	342.496481	2195.176070	32.647279	2537.769475	234.606307	1635.748112	354.726039
VGRPEWWMDYQ	1576.20734	194.14535	290.41313	2883.99019	1146.92306	93.87076	414.79107	1182.11348	59.69806	1044.90969	538.58583	91.43706	2189.47047	500.89876	34.85741	2217.47079	1082.51020	692.61064	364.10686	1380.17678	3469.47448	492.82349	311.33460	4506.21015	275.73693	290.15964	261.04911	8588.15190	1765.14136	4241.82191	30.50751	3544.10994	281.37865	532.18759	1811.29347	6577.05084	54.82817	783.17879	156.95785	1422.94433	134.84422	2906.92131	69.05596	1344.79639	322.06240
YGGFMRF	3277.10339	817.54290	530.96136	3158.43671	1889.17766	350.22889	199.13685	1265.65336	255.36544	506.28135	234.27645	285.55386	1787.88402	249.74974	339.10431	3665.53463	818.74130	803.81119	299.57420	1247.54311	3822.77048	573.19692	161.20958	3638.78731	586.95171	632.28774	231.83586	5510.94689	153.26428	4094.95237	97.02076	5434.93802	291.04362	263.25184	4676.60855	12708.79053	1526.62314	1372.28072	843.84629	4037.53577	137.36138	752.83447	98.67721	323.92474	246.63997
YGGFMRGL	1836.90342	532.37160	31.91848	2847.27001	1856.90606	404.48354	97.22700	677.66059	33.53752	645.95926	282.21996	387.94176	1286.48940	205.61986	166.53826	2640.89078	296.69875	496.77169	200.56853	808.32222	3231.73725	122.02982	189.88514	3470.21471	368.73299	472.46898	348.11946	6392.58899	3404.71172	4530.36369	244.53956	3898.54613	144.88582	108.68853	2560.76269	9825.77789	688.96373	2033.99948	486.94994	1296.00442	173.35597	1444.34044	279.74256	549.30488	1162.47318
A(+42.01)AYKLVLIRH	798.60588	1480.54719	725.73721	71.60675	228.42121	272.31054	807.73288	93.96281	779.88305	486.05579	208.16934	1937.37244	561.45037	1419.84218	1530.09547	2063.12921	709.47529	459.28383	707.09421	630.99962	843.55157	2178.03669	710.63027	775.49936	813.49807	466.42727	1923.66008	1869.92994	148.17764	839.10722	2665.53447	353.48473	654.00743	2585.00058	217.41522	1431.72693	4320.29357	2838.80788	1304.84701	1061.99826	1143.93057	791.25816	1152.74140	705.43317	1275.19600
A(+42.01)AYKLVLIRHG	838.4239	1581.6833	782.6348	969.5311	2301.8224	761.3239	707.8753	135.9221	133.4806	968.4294	892.2048	1550.8702	743.0201	1183.8732	1313.2090	1497.7171	1156.7555	397.2330	570.2994	555.7789	887.6843	2373.2036	457.8341	1982.4404	473.7134	1345.0662	1702.5099	1951.0980	116.3505	756.5601	1268.9385	280.0465	1491.3421	2616.0699	342.9678	1684.1358	4187.7815	3285.8834	1558.2654	570.3506	940.3492	1463.0429	919.2417	1519.9670	2957.6570
A(+42.01)AYKLVLIRHGE	857.11585	852.70201	716.20598	526.75251	1051.21058	596.45370	769.07849	58.90178	552.33074	646.66268	716.87498	805.43845	564.55017	1170.96837	1447.28774	955.62648	1784.60533	183.19341	715.41063	322.42516	561.02695	1832.46351	665.82320	976.34427	1254.15867	952.62062	2364.61748	900.65080	931.57022	346.38412	2493.37072	349.91676	1000.32955	2082.40757	62.88033	988.78026	3979.44604	2913.58368	1869.65159	618.70290	1283.68898	420.62117	634.43863	616.99351	1851.50337
TYNFAVLKLMG	74.59739	777.95787	15765.50869	851.41842	1012.87726	1195.73373	5749.66487	1237.76591	440.03468	1011.40372	256.63578	2148.36209	1485.58455	4921.21572	877.41128	207.69653	7821.67898	40.57287	1541.99540	1197.72656	3849.76712	4847.81657	3195.12239	119.49809	4877.31651	4457.60296	4943.57905	100.01545	878.63435	133.58218	4987.46394	64.10139	538.21704	4774.40368	18.02188	72.58688	54.46752	370.75385	794.98062	144.32519	3058.70554	545.43964	818.20736	740.07192	358.10144
TYNFAVLKLMGRG	18.884222	19.958153	6240.010721	162.153630	65.087173	406.999395	3015.241339	705.712845	32.320475	381.698703	318.654909	941.238647	16.617846	3133.874574	313.808823	128.929168	4501.956868	22.385266	1068.197471	32.481974	1368.420984	961.492064	1214.515233	7.278213	2816.114720	4734.678625	1048.204681	36.688754	319.294236	1.298602	1368.948154	20.323870	48.081600	3549.688174	2.264871	26.512488	23.025668	219.859446	601.029814	27.578303	2316.844684	1.684240	319.697271	3.160324	801.660186
TYNFAVLKLMGRGTKF	198.53037	908.08110	788.19118	505.21446	1002.18749	840.39381	721.93455	18.76126	210.10601	2139.39143	431.74544	1354.78742	183.23786	1211.43447	726.55089	1898.04399	2873.67236	317.29886	4450.13935	54.88774	118.33900	1490.66305	1187.58124	783.52794	1131.91624	5560.59013	938.02302	62.27790	710.62571	786.49201	1106.91702	1123.42344	823.68863	2306.56483	82.92159	379.34814	999.56205	1139.22298	4711.85021	1272.19713	399.75195	196.98868	1153.52185	118.85749	1015.56160
EIGDEENSAKFPI(-.98)	1007.03995	428.90190	1237.33629	2374.48912	1424.32043	232.87716	373.89955	692.62220	270.37067	516.58247	234.07642	47.73324	2882.95298	383.46514	519.77714	1565.73396	480.00881	531.12968	284.68001	840.67184	5321.86021	572.57580	337.76794	1815.82325	384.58549	478.68962	59.60124	1906.97678	2124.65561	1628.36899	419.28977	2745.35107	16.88981	237.80851	4011.04489	3965.49934	1080.65168	773.25013	502.46814	1983.42093	256.57014	1697.65461	553.07489	4428.52412	1045.16567
SFFAVMGA	908.964048	21.411416	6629.147853	320.093546	109.242547	664.758843	3370.841903	820.589019	318.358593	754.935210	72.160460	103.630719	416.322060	7332.037531	894.030389	68.894524	5014.265351	1943.466525	1184.351966	817.220559	1659.718994	1276.144677	1084.565182	1.694142	2960.018035	174.455403	4004.800487	75.459577	443.111473	63.982989	2506.758310	32.277469	910.277812	3756.159548	18.257363	58.708481	96.115232	135.368347	200.017764	194.325490	2269.718841	1559.730531	1651.391857	1525.808419	1268.588161
MQIFVKTL	9694.81793	1735.10771	752.25839	2493.00934	1757.82547	625.97692	456.98751	2654.65458	158.65426	183.98327	1312.41554	1797.81132	1247.65184	483.66960	1278.48191	1137.35178	778.49499	478.74225	422.69241	487.36697	795.63970	1308.65186	264.29153	2043.34129	763.77974	554.69321	240.64482	1758.88205	77.01793	992.75352	447.41691	1006.31357	59.92123	1717.47891	190.38181	629.49869	2819.36221	1920.25238	764.80607	1263.58084	315.38174	491.30568	419.40746	423.43660	1553.92703
MQIFVKTLT	4598.6416	1025.2667	175.0279	748.6038	1820.7397	90.8573	259.4376	1986.7273	464.8169	290.4490	927.2175	1593.8032	2057.8184	427.4547	1375.8753	1180.2505	656.5838	538.4611	236.8635	328.9365	1934.8940	1410.2822	600.1619	5599.2504	2173.1695	1713.2377	1994.4105	3864.2950	281.3795	1062.0775	2151.0122	1051.2226	1180.2403	1240.1931	1388.6237	2396.2311	2745.9394	1292.6257	201.6553	1966.4812	1188.5625	108.7402	808.0423	107.1082	1087.7308
MQIFVKTLTGK	4711.83204	1643.05263	208.44368	139.90212	683.98322	258.18090	201.10243	2662.74111	102.18709	157.10167	409.29318	1558.55846	1456.64097	235.55152	44.34624	1004.51945	204.79361	445.27450	686.74458	214.49328	1130.57539	907.34456	130.73188	4517.82296	388.05727	2652.64315	412.94586	4898.03908	356.13981	1680.67146	146.92267	562.02118	359.89028	382.91044	241.89481	1733.23131	4547.54562	3374.31103	234.10321	1338.85683	94.60629	874.87559	898.93289	264.56131	3754.76799
STLHLVLRLRGG	7435.2517	1226.1263	912.3298	465.6819	510.3557	657.7270	1191.4834	2750.8814	1106.0386	745.4280	1925.2674	1638.7451	1914.2717	302.3996	2226.9619	405.5123	425.7428	745.7822	1067.8206	632.0172	821.0392	1237.2539	716.6066	1930.0519	1617.5934	2436.3303	1030.0996	1404.3968	768.9529	752.7732	973.3351	914.6688	742.2882	809.7576	1062.0042	638.0323	1310.9679	1261.4616	2613.8312	501.0591	827.7549	565.8845	1307.0926	789.9503	2397.4183
TLHLVLRLRGG	15719.8978	149.7432	186.6167	362.0543	331.7471	992.2801	2228.7394	1737.2681	222.0377	665.9341	3636.7218	1555.8034	2503.9958	392.7418	3966.7928	436.9444	508.6143	648.6209	436.1338	669.4793	956.2199	1472.4422	992.2719	1224.7195	1791.4931	2185.7271	806.1279	710.5432	631.0074	529.3217	997.1974	526.3743	1065.0811	951.6614	103.9640	559.1731	1240.9332	659.5764	2593.9575	676.7960	1566.0221	328.9800	1271.1553	600.1839	2825.9162
AFVLVLYDELKKVI	1032.15916	1800.33331	3717.37485	277.66143	5056.79611	2924.26629	3073.53080	53.32718	937.58706	2178.69012	4550.02888	1879.75977	47.13454	4929.29501	2561.43458	1404.31034	8840.65567	1251.42391	9070.68097	2232.15622	5476.36348	556.13221	3112.89528	951.94976	5055.87289	67.27725	2320.64958	565.11431	2773.21077	2286.23384	9399.29825	220.16747	8551.37601	24525.28460	1208.15747	586.51248	1799.31261	1741.93498	498.54584	3651.38420	2950.58813	2381.66271	23833.45667	2401.36262	1312.90416
GAFVLVLYDELKKVI	1161.37054	1840.10319	3488.07381	1163.97084	4501.93462	4069.58151	2878.49495	115.21818	1036.84592	3806.20936	33.01498	194.14648	1513.68036	4773.55340	191.65834	1207.11398	8464.07725	941.93907	7337.71792	1322.39982	7132.23103	1067.10908	1918.41048	1297.57077	4224.30985	1618.62751	2266.41253	667.35177	3095.99246	3044.81164	13216.01530	789.06543	10061.03594	44202.69848	1372.32370	1274.95884	934.74362	3092.23819	1555.97017	5433.68714	4045.93641	1175.98272	27246.52232	619.11009	112.75911
M(+42.01)DVFMKGL	5547.295079	604.282416	1388.073545	60.554151	1095.708735	1936.388836	1467.235592	1219.957490	1924.303972	722.400338	304.183530	2390.948960	1033.573117	1468.443362	1547.412948	929.015712	901.448091	570.345227	522.237086	1484.796384	160.383198	4976.241746	2199.091844	1152.764148	1385.472699	1807.871470	5787.921058	896.506672	32.020463	455.049351	4955.307603	329.951113	4070.264978	3268.110628	3.504012	221.042502	2647.903204	3048.016342	2380.878247	279.456893	2160.559091	174.428253	3614.398015	345.014877	5825.098742
SHLGGAVF	2017.38172	122.22267	1272.89279	26.74408	1052.67238	239.32207	2002.10239	14.53087	615.96783	162.28684	256.58235	2516.86117	518.31921	1792.92716	1700.80309	106.57597	839.31277	205.11420	48.18888	112.59668	145.80708	2961.81619	624.22806	54.41184	739.09697	2143.72569	2516.44753	603.00866	437.31817	320.22138	1092.40441	134.60532	1308.79630	310.29545	9.12582	18.17970	1348.44989	375.75794	1724.13985	34.55316	1866.19923	933.47383	391.72594	106.54388	2257.03394
APIGLKAVVG	688.7594	880.8430	1288.4240	898.2885	1992.0111	657.5115	1489.8485	131.0883	622.6259	438.7437	630.3957	592.9916	1037.2821	546.2257	598.7059	1008.6210	1870.4417	423.9292	404.4216	288.7757	842.6012	2575.6674	567.0160	1237.3554	757.3971	938.4079	1047.9448	1750.3194	1128.6649	628.0263	2336.5318	918.9712	1060.0797	3383.1631	1390.9445	3329.2687	4508.0602	2701.2430	727.4268	2239.0586	1112.6110	1029.9512	947.4633	548.8296	1236.5564
ALNSVAYERNAMQNY	2078.75169	287.39367	107.19245	4265.21067	4918.47142	553.17164	153.76952	769.55449	499.29604	1068.53435	1107.42338	219.75415	2702.47638	152.58235	441.44409	3308.82327	76.13406	195.96705	187.04968	953.96434	2176.91668	1038.62363	92.11280	4156.26417	332.56684	754.63501	241.97156	4017.93379	1875.33209	3481.40951	649.54016	3015.54867	32.42745	170.48844	1046.59917	3977.14762	451.37023	521.90575	194.35964	2545.26702	171.15992	925.80961	99.87891	1613.25856	46.18628
ALNSVAYERNAMQNYE	1853.83835	319.67984	19.83804	3512.28318	2260.89293	299.84896	114.77209	591.46572	310.00070	1258.52052	74.61045	137.80235	4021.27123	143.03839	223.08775	3772.48112	478.19398	543.02017	145.04854	987.84315	6492.47744	24.88639	295.72032	3188.91508	11.27708	229.89036	98.46039	4061.46298	2714.35087	3967.16883	43.22053	3615.50712	40.56923	18.22028	1539.10872	4565.99766	377.45222	808.38962	602.15155	3060.13219	46.72943	1298.84604	347.23508	2054.86247	606.21722
RPKPQQFFGLM(-.98)	2007.6241	254.3768	118.5551	2262.6295	1970.6317	216.1109	177.3325	1189.8959	307.4361	502.1439	801.6248	506.3732	1960.9191	305.0199	517.6350	4017.2061	926.2380	582.6733	275.9592	893.4542	4390.7067	299.7748	217.2125	2665.8498	854.7283	1496.5060	273.7496	3348.7888	1286.3264	2785.6858	650.9505	1675.2608	156.0367	936.2377	1773.9998	2436.4518	933.9509	826.9920	1010.8450	1418.1266	197.7681	284.7328	162.2780	586.4644	506.6594
S(+42.01)DKPDMAEIEKFDK	7915.10502	947.48300	436.95779	427.55725	565.05539	323.16191	535.20512	2065.62482	310.46879	683.82121	1545.49875	736.74700	3362.78613	84.80612	922.06293	1254.90791	372.14090	661.73503	487.70809	677.17053	1548.34254	863.31329	658.50306	2042.15894	488.90273	1531.17518	510.28772	2176.44570	278.11973	1180.40785	679.03509	1229.59984	834.22361	88.99058	272.56688	1814.71198	2919.51286	2645.74389	2007.26101	1761.84978	281.58952	914.26676	961.51688	2152.27217	4478.86515
GASLKPEFVDIINAKQ	3419.24217	2641.51142	84.73763	375.73393	4858.61102	699.07087	336.63764	184.52915	739.27489	538.34718	1152.66170	2557.40047	810.26010	323.68948	774.16014	1583.99595	642.46031	314.54642	625.43202	47.93779	1514.67068	1101.57552	1372.35879	5948.21746	862.05389	1674.18389	954.03336	3671.34853	1414.35664	2498.08842	948.66523	1997.07341	1207.77574	109.95835	1334.82335	6419.89803	8716.65575	3188.29317	2573.91185	2504.98467	1525.41821	80.66622	4212.06458	1031.92743	5762.55632
SLKPEFVDIINAKQ	2307.09058	1174.70246	346.67141	94.95867	1803.57973	906.28715	731.46227	186.70226	490.25434	785.12329	352.66208	219.12464	1277.71560	573.70022	670.05642	817.34916	887.71831	378.71909	692.04318	626.10780	682.83450	305.35842	834.67203	1511.16077	927.97933	2460.74434	2043.23786	1052.58291	180.61451	734.82967	1749.14102	691.40981	586.24931	575.02803	121.62135	1577.79128	4753.60289	3967.12899	2544.04104	837.22645	1264.45631	569.74308	1870.43001	427.50410	5673.58304
ASWTREPLE	586.51615	623.54925	179.55599	948.81491	2656.13828	711.09383	437.68457	676.23984	85.91239	1345.47131	22.08135	450.81523	1199.55683	184.15843	114.85261	1979.76433	528.15320	1066.04219	609.73444	490.27839	4060.08935	168.96416	416.24479	1648.63804	163.92009	21.50038	685.20938	2555.42881	2084.44188	2056.79530	774.88690	3633.98939	285.88187	508.05511	5025.12407	7762.68442	790.45648	642.91603	441.49810	4734.88644	228.29318	1275.83941	372.06649	820.49451	103.94815
ASWTREPLEE	13.79051	752.95749	1103.14568	634.88200	1304.62163	219.80147	4180.86328	890.78925	490.96352	623.38148	1006.64314	424.78734	1147.22953	180.43248	215.31349	1396.46218	1004.62611	772.00266	581.68549	578.53459	3058.03395	85.75380	164.82972	1086.04356	111.74000	733.37171	870.73307	1786.42741	1317.40686	1501.28563	85.50301	2054.15688	79.28791	899.67912	2863.75884	4884.59999	189.85796	522.92978	467.56626	3520.69327	468.92531	875.86207	192.11117	653.35465	175.75263
EDEAAWSLDRTQQ	968.78650	493.19557	381.52423	603.31701	1424.47905	149.90087	156.46713	834.95647	197.79212	676.89241	429.70441	386.25403	2327.97645	209.96372	363.66514	964.81028	414.09816	1327.69861	363.88604	937.30376	5804.36880	55.99629	210.20380	2002.88703	231.89297	21.98958	265.83543	2344.13006	2125.73545	2035.20696	601.24231	3529.88163	337.20592	63.57975	5774.16131	8195.42772	504.99511	280.17946	261.99040	4985.39337	78.88509	1497.82726	260.97273	1284.50564	140.35012
FLVFHSFGGG	566.73550	202.55941	492.43685	382.37004	1129.86727	291.52958	106.90036	1423.27461	70.17791	1731.09851	1410.40598	1061.18617	41.28055	1042.75255	615.91410	1827.10144	4178.38016	64.20077	5360.04785	62.22662	2154.63213	2722.43062	144.73699	1234.99894	177.22113	2112.59983	4606.81806	424.95340	1251.32359	808.18434	3358.76133	493.33324	58.80551	527.67807	87.64082	148.33594	160.53909	2415.26223	737.99890	548.80400	757.92821	265.69176	2271.68956	206.55926	866.70523
GLQGFLVFH	702.41719	834.03146	4418.77047	11.22520	642.48453	1034.26925	1851.96400	39.62615	537.78980	576.44001	55.20495	2257.51417	352.36579	2766.19550	979.86395	218.58094	2280.66447	83.40495	704.64233	745.81890	1052.42113	1425.23238	706.74213	55.43628	1180.12484	913.70595	1414.84968	19.19631	345.50211	119.72495	2291.31921	82.89753	1242.22070	2847.69350	796.52450	43.42057	462.25050	873.04826	859.83316	38.88685	1809.07790	18.61412	1015.00933	65.33729	841.27356
LQGFLVFH	97.125405	61.635811	3064.902005	199.427636	326.941368	468.601464	1760.335137	19.996348	421.877723	410.947297	31.084675	371.172918	25.721345	1435.986352	533.071611	168.839839	1891.074912	6.283562	786.523550	22.980673	19.811860	333.636689	683.213912	31.361028	837.533104	469.391850	2533.503779	44.687502	335.534066	11.876638	3840.809392	73.957859	1685.541149	1841.716636	6.370228	117.509457	427.230180	765.450017	483.395165	202.772187	2982.467676	28.777560	909.459278	36.558068	502.656808
SGFTSLLMERL	536.377274	235.205346	1549.979427	243.639537	102.796412	286.577101	1549.788004	4.532093	786.255121	636.677208	8.432415	530.958104	7.652825	2730.046023	655.407552	298.658322	5622.211594	121.017992	2616.048590	1143.994208	3220.841115	428.061256	1125.207820	449.668432	2551.393087	1221.600276	1337.067773	333.541533	833.133896	307.572336	3060.375353	35.797979	1102.960030	16289.294161	2665.737779	361.204148	1557.314673	2780.045418	1411.786512	949.350402	872.206225	185.601595	8862.173214	1199.253187	1442.563700
SIYPAPQVS	139.281572	144.039489	3682.540090	28.116965	297.368691	611.528438	4268.410808	6.432718	90.855333	351.476745	202.459110	469.252810	133.785182	3225.275558	403.904656	33.321078	1942.687335	2014.743852	448.986240	2.526142	1710.145595	2157.707872	1150.319948	42.703295	1606.418866	1101.943995	3723.677289	12.648693	343.754049	105.067247	4626.009386	65.754625	2903.408550	2863.253515	7.374992	83.251196	806.856479	1623.288566	1470.640512	231.406034	4272.149357	15.720285	524.001211	9.884706	134.244822
TGLQGFLVFH	17.0926773	14.8936941	5736.4222002	13.6359213	323.4224011	422.1025717	3626.2317680	3.3047510	489.8051661	605.6506173	43.6174982	206.3361248	14.2226979	4637.0568210	503.4802419	4.6624971	3147.8480186	9.3327409	577.4364153	0.5867166	1.2780913	1436.3678987	1213.7226281	1.1566648	2320.0034821	277.1794519	4271.9184162	7.4244579	247.2758307	55.8592211	3930.8610400	31.8964408	2018.0312733	2164.6437246	782.3407026	5.3243010	81.4101703	193.9286471	485.9210397	74.4629671	2226.5055165	1.7514040	389.8806480	5.5891815	150.5680427
TGLQGFLVFHSFGGG	10.10000	916.96434	2715.49315	527.60816	496.44611	716.52554	2814.01723	1101.44335	1239.04537	2611.53986	186.48715	276.50667	920.10161	5635.64490	179.42601	14.67262	10085.68614	50.44725	2783.19856	130.94280	2227.58803	154.70969	2075.82765	173.04157	1923.95894	691.51545	2792.11089	156.54893	716.50930	191.67665	4791.78413	80.87278	2732.25899	9934.59116	3533.78030	124.81227	143.83455	1878.05079	1925.98910	229.54670	3030.28024	1030.83396	3978.68706	1240.33364	219.88965
TSLLMERL	72.9286616	39.6882069	6548.2786067	99.6780255	145.3954539	255.6151854	3442.6356488	6.4131424	463.0290614	242.9542568	33.5535438	622.8856934	54.9690331	3319.6826862	25.6431093	138.8582488	1524.4732219	25.1642434	923.1111131	25.6618158	29.8525178	1403.9036122	732.6802341	46.1962693	1026.6790175	631.8079961	1583.5571629	106.1829539	7.6245515	32.2310399	3386.7288497	0.7435863	1703.4630594	2964.8209345	36.4210839	96.0426624	702.8678131	256.6200097	184.7343216	32.2534751	684.8203934	40.6133512	83.0861635	18.5816529	23.1350649
SGPFGQIFRPDNFVFGQ	52.54652	29.80969	7182.96651	387.05549	915.04586	2927.20746	8022.00504	854.61714	1358.54183	1167.56739	41.51143	1225.04496	807.87632	13823.88125	94.88643	58.88198	11257.19560	64.94843	3810.20094	113.63357	5628.80080	2270.22385	4785.70726	375.15026	3996.46058	61.65754	6925.96112	242.12964	355.54296	317.00152	3409.20101	204.82363	2054.08835	8257.35639	2242.28016	102.43023	134.97014	997.75867	963.18633	180.30468	1162.62713	290.52011	4668.54492	504.90872	407.13068

Log2 transformation

Data transformation applies a mathematical transformation on individual values themselves. For mass spec data, log transformation is a good choice, as it reduces or removes the skewness of mass spec data.

Code

plot_grid(hist_log2, qq_log2, pca_log2, nrow = 1)

Code

#rownames(log2_d1) == feature_name$variable
rownames(log2_d1) = feature_name$name
# display table
log2_d1 %>% 
        mutate(across(everything(), round, digit=2)) %>%        
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

	Hypo_39	Hypo_36	Hypo_44	Hypo_25	Hypo_48	Hypo_52	Hypo_21	Hypo_20	Hypo_55	Hypo_60	Hypo_19	Hypo_42	Hypo_37	Hypo_24	Hypo_22	Hypo_43	Hypo_35	Hypo_63	Hypo_66	Hypo_54	Hypo_65	Hypo_49	Hypo_53	Hypo_23	Hypo_31	Hypo_45	Hypo_32	Hypo_57	Hypo_33	Hypo_40	Hypo_47	Hypo_58	Hypo_51	Hypo_46	Hypo_64	Hypo_59	Hypo_27	Hypo_34	Hypo_26	Hypo_61	Hypo_38	Hypo_62	Hypo_50	Hypo_56	Hypo_41
A(+42.01)LLRGVFIVAAKR	10.36	9.36	10.13	9.62	10.65	10.41	10.27	6.81	10.59	8.36	8.30	10.81	8.88	9.76	11.30	8.94	9.25	7.84	8.44	6.15	4.35	10.94	9.23	8.99	10.31	11.40	11.36	8.06	9.22	7.18	11.98	8.22	11.58	11.97	10.47	8.60	11.64	11.10	11.40	7.98	11.00	6.64	10.11	8.26	11.75
SAMLIQKL	10.70	8.50	8.92	8.73	9.98	8.52	9.06	4.60	10.46	7.90	9.73	10.77	9.92	9.59	10.41	10.58	11.17	8.72	9.75	8.69	8.84	11.15	9.71	9.56	10.05	7.85	11.64	10.19	6.79	9.45	12.34	9.05	8.87	10.89	9.97	9.89	11.05	11.22	10.48	8.93	9.74	8.65	10.11	8.40	11.13
TDYLMKIL	6.08	3.70	11.99	7.12	6.15	7.75	11.69	9.24	7.60	4.60	3.59	8.64	5.21	11.30	10.08	6.26	9.93	4.14	7.22	3.48	5.92	11.86	4.19	4.71	10.51	8.28	11.32	5.38	3.51	3.34	12.12	5.05	10.90	11.56	9.98	1.79	7.63	8.37	9.03	1.90	11.13	9.61	9.65	9.18	9.27
PYQYPAL	10.77	8.91	10.51	3.57	9.17	8.95	10.25	7.73	9.50	7.55	8.73	10.28	8.59	10.38	10.81	8.70	9.52	7.08	7.57	7.81	6.58	12.23	8.99	8.41	9.85	11.30	11.49	4.13	8.51	6.58	11.57	7.40	10.59	11.32	3.74	7.02	11.02	10.63	10.78	7.19	10.83	5.42	9.51	7.05	11.85
SESLFVSNHAY	11.31	10.21	6.66	6.81	10.32	8.42	9.08	8.98	8.87	8.80	7.39	9.98	9.99	8.96	10.01	10.35	9.76	8.48	8.73	8.67	9.07	10.06	9.17	10.29	9.59	10.87	9.84	10.49	7.49	9.28	10.15	8.95	8.95	9.60	7.45	10.60	11.91	11.70	10.69	9.24	9.04	9.39	10.22	9.65	11.80
SLFVSNHAY	10.98	9.34	8.87	5.69	10.13	8.92	10.08	8.21	9.57	8.65	9.20	10.39	9.44	9.56	10.44	9.34	9.91	7.43	8.16	8.28	7.80	9.59	9.49	9.55	9.92	11.09	10.97	9.10	5.85	8.19	10.88	7.83	10.24	10.00	6.03	9.04	11.35	11.20	11.15	8.16	10.55	7.76	9.91	8.66	11.93
GAAAQSLYIANHAY	9.02	9.67	6.79	7.68	11.55	8.70	8.61	8.76	7.95	8.90	8.39	10.69	9.37	9.45	9.43	10.44	8.76	7.85	10.33	9.36	9.38	10.01	8.71	10.94	9.82	11.00	9.61	10.67	10.76	9.55	8.41	9.02	8.59	12.83	8.91	10.36	11.77	11.27	10.74	9.28	10.54	9.79	10.43	10.30	12.31
SLYIANHAY	10.87	9.21	7.33	6.54	10.45	9.70	9.71	8.13	9.84	9.80	9.90	10.71	9.61	8.27	10.71	9.33	9.83	7.69	9.10	8.27	7.77	9.23	9.38	9.33	9.35	10.33	10.79	9.03	5.60	8.04	10.64	7.92	10.20	9.93	6.07	8.91	11.24	11.12	10.98	8.92	10.66	7.63	9.72	8.23	11.35
DIDTAAKFIGAGAA	7.53	10.38	10.04	8.60	12.05	9.30	6.89	5.83	8.14	10.30	9.71	9.75	10.72	9.47	8.75	10.42	10.91	9.22	11.31	10.23	8.49	9.47	9.03	9.59	8.30	7.87	8.53	9.84	4.39	8.69	7.36	9.16	6.22	11.98	9.83	11.67	11.17	11.83	8.00	12.28	7.65	9.81	10.93	8.89	8.60
VPPVQVSPLIKL	13.67	8.70	9.06	8.90	9.06	8.31	8.08	11.30	8.22	8.98	11.75	11.00	10.15	8.45	10.83	10.24	6.10	8.01	10.01	8.18	9.23	9.98	7.38	11.19	9.38	11.37	9.26	11.42	9.60	9.38	9.27	9.09	8.04	9.08	8.11	9.23	10.85	11.53	10.68	8.98	10.14	9.86	8.93	9.42	12.36
VPPVQVSPLIKLGRY	12.85	10.15	8.87	7.10	9.16	9.48	10.26	10.43	9.65	9.07	11.28	10.88	9.19	10.68	11.77	9.98	8.75	8.42	7.75	8.42	8.05	10.09	10.14	10.03	11.19	12.99	8.45	9.36	9.16	7.90	10.52	8.41	10.18	10.96	10.27	8.63	11.41	10.38	11.77	8.98	9.14	9.34	7.72	7.92	10.26
TIDFPEFL	10.82	6.99	11.66	7.50	9.36	10.03	11.57	9.59	10.53	8.71	6.77	10.08	8.78	11.57	10.90	5.21	9.87	12.00	7.83	7.89	4.45	13.37	11.03	7.07	10.52	10.53	12.88	8.70	8.27	7.06	12.18	6.09	12.48	11.64	6.76	7.18	9.87	10.44	10.56	7.24	11.69	4.68	11.36	3.40	12.82
Q(-17.03)EDAELQP	9.70	9.80	6.10	11.33	9.02	8.90	6.96	9.88	7.13	9.99	4.67	4.42	11.00	8.38	8.87	10.97	8.76	10.93	8.64	10.13	13.13	5.74	6.05	10.95	8.35	6.71	5.94	12.13	11.31	11.43	6.10	12.75	6.59	5.64	13.25	13.87	8.02	8.30	8.33	12.21	4.93	11.45	7.47	10.78	6.93
Q(-17.03)EDAELQPR	9.10	8.66	8.58	10.48	8.70	6.98	7.14	9.16	7.25	9.14	6.19	8.50	10.04	7.19	6.75	9.37	8.62	10.58	7.66	9.96	11.78	8.71	8.12	9.57	7.22	5.89	7.87	11.37	10.57	9.99	8.93	12.00	2.24	4.89	12.70	12.96	8.81	8.24	7.13	12.41	9.03	11.27	9.49	10.49	10.17
SAVISLEGKPL	11.21	9.79	5.46	6.75	10.67	9.15	8.69	8.05	9.05	9.80	8.63	10.42	10.05	8.91	9.30	10.36	9.48	8.60	9.09	8.75	9.68	9.67	8.94	10.63	8.51	11.06	10.40	11.04	7.83	9.18	10.37	8.93	8.36	10.14	6.95	10.38	11.89	11.58	10.24	9.81	8.57	10.06	10.32	9.47	12.14
FLGEAYHHVPESQ	10.21	8.54	8.29	10.84	10.59	4.95	7.16	9.49	3.31	8.67	8.05	3.44	10.64	7.90	8.96	10.00	9.20	9.52	9.13	9.05	12.18	9.55	4.24	10.97	9.48	8.42	9.33	12.19	12.58	12.12	10.38	12.98	8.75	9.43	12.41	12.23	10.96	10.54	10.35	12.38	10.24	9.92	9.00	10.54	10.54
FLGEAYHHVPESQRD	9.79	8.87	8.31	10.85	10.59	6.78	7.16	9.59	5.00	8.84	8.28	6.88	10.97	7.58	7.99	11.10	8.66	9.80	7.37	9.81	11.39	8.54	7.45	11.30	7.62	8.61	7.65	11.51	11.66	11.42	2.56	11.83	5.28	2.53	11.99	11.64	10.28	9.15	8.52	12.14	9.03	9.95	8.59	9.33	6.88
LGVLFNPYYDPLQWKSSRFE	11.05	9.13	7.76	11.63	11.28	8.87	9.10	11.78	9.57	10.31	8.38	7.31	11.69	8.59	9.24	11.44	10.13	11.03	9.82	11.93	11.94	7.01	9.91	12.57	9.92	9.19	8.28	12.84	12.11	12.14	9.35	11.89	8.03	7.79	12.02	11.45	9.84	9.86	9.50	10.82	8.90	9.82	9.46	10.94	7.37
Q(-17.03)YDRVAELDQLLHY	11.17	9.74	6.85	12.22	11.42	9.41	8.91	11.62	9.09	10.36	7.98	8.22	11.78	8.91	8.58	11.91	9.63	11.54	10.06	12.31	11.80	8.82	10.17	12.92	9.60	9.29	9.43	13.66	12.41	11.37	9.61	12.03	8.62	9.17	11.80	12.04	10.28	10.24	9.61	12.04	8.77	10.37	10.39	11.02	9.93
SVLISLKQAPLVH	11.48	9.30	8.96	9.04	10.17	7.82	8.66	8.06	10.52	10.13	8.83	10.22	8.86	10.21	10.74	9.68	8.37	10.55	8.15	10.53	7.71	10.50	9.75	10.18	9.67	11.68	11.13	10.67	10.03	9.76	11.19	9.12	9.77	10.06	9.59	8.83	10.31	11.40	10.96	6.98	10.44	9.39	8.44	9.15	11.91
TTMIIDHVVPEPG	9.36	7.47	12.00	8.72	9.14	9.30	10.99	9.82	9.37	10.02	5.30	8.66	9.76	10.84	9.67	9.30	11.16	10.97	10.57	3.58	10.89	10.23	9.36	8.57	6.64	10.48	11.13	7.17	9.43	8.56	11.39	7.85	10.26	9.63	9.94	6.43	10.90	11.29	10.02	8.51	6.03	7.35	11.35	7.68	12.05
TVVYGEPITA	9.26	6.74	10.25	2.69	8.53	8.27	9.72	9.30	7.86	6.43	5.46	8.76	8.33	10.66	10.13	7.91	11.49	5.81	8.83	4.86	4.01	10.83	10.17	7.06	9.72	10.65	11.03	2.64	9.10	3.28	11.08	3.69	9.13	11.45	4.86	5.29	9.15	8.24	8.54	6.52	9.63	2.09	9.39	2.86	11.33
S(+42.01)ILKIHAREIFD	10.76	10.03	10.14	5.59	11.36	10.84	10.27	8.39	9.29	9.78	9.10	11.31	9.96	10.74	11.54	10.76	11.36	9.63	10.22	9.57	8.19	8.33	10.26	10.89	10.76	11.66	10.16	9.80	7.96	10.05	11.67	8.90	10.12	12.00	7.67	9.11	11.58	10.45	11.59	10.04	10.45	9.02	9.67	8.76	9.68
VKVGVNGFG	10.60	11.15	10.59	5.44	11.73	9.61	9.08	10.00	9.36	10.17	8.40	11.01	10.56	5.98	10.48	11.02	7.42	9.33	9.47	8.89	9.04	10.98	9.15	10.65	5.73	8.67	8.61	11.11	8.50	9.98	8.48	9.77	8.99	9.00	9.36	10.83	11.40	11.28	9.56	10.26	9.13	9.90	10.41	10.00	11.95
VKVGVNGFGR	9.74	10.08	9.02	9.25	10.67	9.11	10.09	8.67	10.55	9.71	10.22	11.03	9.61	10.65	11.30	10.07	10.76	9.76	8.53	9.60	9.87	9.56	9.68	11.13	10.26	11.34	9.53	11.60	9.04	10.32	10.41	10.57	10.84	9.53	9.80	11.65	11.29	12.67	11.08	11.52	10.86	8.72	10.69	9.30	11.08
VKVGVNGFGRIG	10.21	11.16	9.22	6.48	12.23	10.10	9.25	9.40	9.58	10.58	8.69	10.03	11.06	9.32	8.32	11.42	9.46	9.78	9.81	9.14	10.13	8.54	9.37	11.01	9.21	7.12	6.64	11.44	8.66	10.50	8.19	9.78	8.67	9.47	9.36	10.92	11.27	11.27	9.81	10.52	8.60	10.20	10.56	10.35	11.99
SGSAKVAFSAIRSTNH	10.85	7.56	3.84	10.79	10.25	8.56	7.68	10.30	8.65	8.40	9.12	9.10	10.43	7.68	2.74	11.14	7.07	10.30	7.69	9.35	11.15	9.09	8.91	11.16	5.07	5.25	8.39	10.70	10.90	10.99	9.50	11.78	8.52	8.77	11.53	12.13	10.25	7.99	8.88	11.07	8.89	10.23	3.48	10.03	9.44
A(+42.01)GQAFRKFLPLFDRVLVER	12.54	8.94	9.37	9.34	9.08	10.90	10.70	11.17	10.00	8.89	10.02	10.77	10.44	10.81	10.39	10.31	10.82	8.47	9.72	9.14	10.01	9.90	9.96	9.15	10.91	12.20	10.57	9.45	9.65	7.40	10.86	9.52	10.37	11.16	10.09	7.68	11.21	11.34	10.83	9.78	10.00	7.03	11.42	8.17	11.11
DILGKYVD	14.76	11.42	9.82	10.65	11.05	10.26	9.08	11.61	8.82	9.43	9.86	11.90	11.19	9.40	7.66	11.05	11.46	8.27	9.70	9.11	10.39	11.22	10.80	12.24	11.44	12.66	10.81	12.36	10.55	7.47	9.31	10.05	9.87	10.57	9.34	11.21	12.48	12.86	11.16	8.99	7.97	10.54	11.10	9.67	12.77
AEALERMFL	10.20	7.82	9.86	7.59	5.95	6.76	9.11	7.14	9.28	5.57	8.90	12.70	7.51	1.94	10.64	6.22	8.90	10.67	6.51	4.99	0.91	10.46	8.15	6.51	9.01	10.45	10.87	7.87	8.78	4.88	10.36	3.29	9.55	10.53	8.83	4.22	9.04	10.63	11.37	8.21	11.54	9.59	10.12	7.11	12.10
GAEALERMFL	10.11	8.08	10.27	5.44	6.64	8.20	7.76	8.20	10.30	9.31	9.00	12.64	7.95	9.26	10.94	4.47	7.51	11.12	5.19	6.22	8.92	12.86	8.87	6.16	9.31	11.76	11.23	7.38	0.75	5.85	10.57	3.79	10.10	9.90	4.47	6.29	9.09	10.47	11.47	5.21	11.37	4.94	9.97	5.80	11.53
PVNFKLL	9.62	6.82	9.20	5.31	5.92	6.62	8.48	8.22	9.70	5.47	9.51	11.56	8.36	9.76	11.52	6.16	6.18	4.05	5.80	6.43	3.59	13.81	7.59	6.39	9.85	12.15	9.09	6.44	8.56	6.81	11.30	5.07	11.03	9.90	9.20	5.15	9.56	8.96	10.37	8.07	11.09	3.86	5.92	5.69	9.31
SLDKFLA	10.39	5.78	8.71	4.17	6.45	7.31	8.62	5.10	9.81	6.92	9.46	12.64	9.27	8.61	10.91	6.87	8.66	4.06	5.93	4.75	2.75	11.91	8.87	3.69	9.57	10.81	11.18	5.60	2.61	6.58	10.37	5.32	9.61	8.62	-0.05	4.32	8.26	9.58	11.09	4.70	11.52	4.45	8.94	5.30	11.33
SLDKFLASVSTVLTSKYR	10.49	11.66	6.35	9.91	10.84	9.47	4.31	12.47	8.62	7.38	8.33	13.36	9.14	7.91	9.05	10.14	5.56	9.35	7.57	9.64	6.48	9.74	7.19	12.36	7.65	9.68	5.94	12.29	9.35	10.70	7.45	7.34	9.12	8.95	6.19	10.69	12.74	12.61	11.31	5.56	10.31	9.96	11.57	11.04	11.77
SVSTVLTSKYR	10.00	10.40	7.18	7.26	10.63	8.60	7.25	11.45	8.19	9.06	8.73	13.43	8.91	3.85	7.84	9.12	6.94	7.42	6.41	7.98	7.36	6.30	7.52	10.65	7.60	11.23	7.46	10.99	8.14	9.62	9.86	8.36	9.53	8.42	6.84	11.02	12.34	10.50	8.95	8.37	9.59	8.84	9.34	9.92	6.64
TPAVHASLDKFLA	10.89	7.25	4.54	7.60	5.88	7.74	7.99	7.52	7.97	6.73	9.40	13.38	8.60	9.11	11.56	7.37	8.47	11.33	6.85	5.23	8.69	11.03	8.83	7.11	9.58	12.37	10.47	6.73	0.97	7.08	10.14	4.38	8.40	10.54	8.73	1.95	10.71	11.27	12.43	5.06	11.67	11.11	11.28	7.91	13.56
TPAVHASLDKFLASVSTVLTSKYR	10.74	12.31	8.42	10.78	10.55	9.10	7.65	12.70	8.48	10.36	8.60	13.53	8.45	6.44	9.37	9.23	5.99	7.69	9.44	9.11	7.03	9.39	8.90	12.15	7.25	9.02	8.41	11.26	8.08	8.06	9.18	7.63	9.05	6.90	9.62	9.26	12.57	12.06	10.07	9.76	8.36	7.58	10.19	9.96	11.42
TYFPHFDL	9.29	4.48	9.43	5.46	4.57	6.54	8.76	5.48	9.74	5.60	8.44	12.01	6.96	9.32	11.23	3.89	7.18	10.98	4.85	4.70	0.22	12.73	8.18	4.74	9.29	10.33	11.29	3.96	8.04	5.27	10.81	5.11	10.80	9.27	8.73	2.32	7.33	9.20	11.45	2.19	12.34	1.05	8.43	2.31	10.74
TYFPHFDLSHG	11.42	7.75	7.71	5.33	8.22	7.96	8.13	7.26	9.68	7.04	9.60	14.26	9.11	8.70	11.33	6.94	6.66	4.57	6.63	5.94	8.17	10.47	8.89	7.40	6.35	12.13	10.50	6.55	9.40	4.93	9.99	7.65	10.19	10.38	9.18	6.86	9.80	11.38	13.12	5.90	12.82	9.39	10.03	5.65	12.98
THYKLVPHQFAH	12.44	8.11	7.40	7.02	9.13	9.79	9.89	9.30	10.34	8.70	11.15	10.73	9.74	9.34	10.73	9.90	9.45	8.51	9.38	8.87	7.61	9.57	9.96	10.06	9.37	12.41	10.25	8.87	7.43	8.77	8.41	8.69	9.16	8.05	4.58	8.18	11.35	11.05	10.91	9.05	10.41	8.26	10.10	8.37	11.82
TAYAIYELAKA	11.24	9.53	9.10	8.44	6.90	8.72	9.97	7.43	10.45	8.40	9.60	11.74	9.95	10.14	11.19	8.64	10.53	6.90	6.88	7.68	6.76	10.67	10.06	7.45	10.49	11.06	10.74	5.94	9.11	5.18	11.33	7.98	10.02	12.10	10.27	1.56	10.47	10.58	12.04	10.11	11.41	4.23	9.72	9.43	11.87
TAYAIYELAKASFPKKQD	10.97	8.97	8.88	9.04	8.69	9.63	9.00	9.87	9.36	9.40	9.36	10.87	11.17	9.04	6.97	10.63	8.73	11.17	9.55	10.65	8.53	10.56	9.81	12.18	9.99	12.15	9.59	10.48	8.19	10.72	10.80	7.91	9.33	9.81	10.44	9.76	13.43	11.98	11.03	10.28	7.25	9.32	10.56	10.08	12.50
SGFAAPFFIVRHQLLKK	11.58	8.86	10.62	8.25	11.96	11.44	6.26	9.53	11.11	8.89	7.69	10.92	10.74	9.62	10.97	10.48	8.50	9.48	7.09	9.46	9.10	9.63	9.28	9.80	10.48	12.81	9.08	6.92	6.54	9.86	10.63	7.85	10.76	10.76	10.07	9.32	12.44	6.81	12.50	8.20	9.09	10.02	8.19	9.92	9.36
AFQKVVAGVANALSHKYH	10.83	11.02	8.69	8.09	10.57	7.88	7.82	9.72	8.67	8.05	8.63	13.21	8.60	8.02	5.81	10.28	9.02	11.28	9.75	10.33	8.67	9.95	8.86	11.30	9.15	10.87	8.42	11.77	8.23	6.56	10.25	5.46	9.20	9.96	6.71	10.88	11.16	11.66	11.84	5.06	10.03	9.17	6.81	9.61	11.02
KVVAGVANALSHKYH	11.13	11.96	8.54	9.05	11.25	9.39	8.31	11.11	8.83	5.27	8.39	13.26	9.12	7.39	9.70	10.65	9.15	8.22	8.50	8.71	7.72	9.82	8.77	10.76	8.65	10.73	8.97	11.07	8.12	9.69	7.14	8.64	9.02	7.53	4.28	10.97	11.84	12.00	12.29	8.49	9.87	9.30	10.16	9.83	8.05
TPEAQAAFQKVVAGVANALSHKYH	10.69	11.01	7.75	6.99	9.76	8.94	7.05	10.24	9.75	7.81	8.04	12.89	9.07	9.01	10.33	9.02	8.26	8.32	8.05	8.42	6.56	8.18	7.30	10.06	8.73	11.39	9.50	10.47	7.17	9.08	8.71	7.56	7.20	9.92	4.99	9.15	12.16	12.27	12.69	6.89	10.24	8.77	11.68	9.68	11.46
RTLYGFGG	11.38	10.46	9.01	9.03	11.29	9.31	8.76	10.55	8.98	8.09	8.61	10.71	10.17	6.64	9.17	10.50	8.57	8.39	7.97	8.69	9.82	9.48	7.84	10.83	8.47	10.29	8.23	11.00	8.00	9.72	8.86	9.48	9.06	9.14	10.01	11.71	12.05	12.06	10.26	10.07	9.86	10.16	9.57	10.32	12.38
TLYGFGG	11.15	8.66	9.14	9.20	8.77	9.26	9.81	9.00	9.27	8.20	8.99	10.21	8.43	10.55	10.17	9.20	9.58	7.11	8.31	6.05	9.59	11.66	9.14	9.34	9.43	10.56	10.97	10.00	7.81	8.43	12.11	7.94	10.67	9.49	8.48	8.56	11.01	11.11	10.83	9.21	10.96	7.74	9.60	8.52	11.40
TLSKIFKLGGKDSRSGSPMARR	11.73	9.84	9.28	10.01	9.60	8.67	8.75	8.60	8.52	9.49	8.59	12.92	8.77	8.96	9.15	9.86	10.13	7.68	9.92	9.89	7.10	11.69	9.10	11.81	9.46	13.15	10.16	11.02	8.46	10.66	10.76	7.18	9.47	10.04	10.17	8.62	13.07	12.28	11.29	10.61	10.82	7.95	7.37	10.02	12.88
SIGRFFG	11.58	5.72	9.53	4.87	6.36	6.45	9.83	6.41	8.24	5.76	10.91	11.55	7.18	7.92	11.77	7.72	8.61	3.84	5.64	6.72	9.00	12.54	8.94	6.74	9.68	12.85	10.34	6.98	3.24	5.00	10.36	3.69	9.58	9.04	8.01	3.57	8.50	9.36	10.05	2.98	10.26	9.55	7.20	0.88	13.01
SIGRFFGG	11.63	5.18	9.39	4.85	4.12	7.23	9.21	6.49	6.77	3.76	10.41	11.44	7.18	8.06	11.32	7.08	7.41	2.83	2.88	4.26	3.67	11.93	8.80	6.54	9.39	12.94	9.50	6.49	8.82	5.37	10.59	6.14	9.74	7.71	1.92	2.59	8.49	9.41	9.55	0.11	10.61	10.03	6.31	5.88	13.45
SIGRFFGGDRG	12.16	6.79	8.97	8.52	5.99	8.11	9.57	7.89	9.50	7.36	12.47	12.06	9.69	9.15	10.83	8.90	9.43	5.94	7.35	9.83	7.47	10.14	9.87	7.74	10.02	11.00	7.72	7.57	9.04	6.06	9.62	7.73	8.06	9.32	7.63	3.75	8.44	9.64	10.68	6.27	9.49	5.26	7.46	7.52	9.54
PMFVVNTNVPRA	10.93	9.58	8.19	3.52	10.98	9.49	9.11	8.03	9.53	9.80	7.49	9.23	9.92	8.03	9.68	10.40	10.32	7.63	8.23	9.07	8.99	7.40	8.87	10.76	10.65	10.99	10.71	10.90	3.36	9.28	10.57	9.50	9.38	11.57	10.41	10.68	12.44	12.29	11.24	10.09	10.22	9.72	10.79	9.47	11.83
SSPETLISDLLMRESTENVPRTRLEDPSMW	7.16	8.75	9.44	10.19	11.93	9.13	9.61	10.58	9.14	10.62	9.30	9.44	11.23	5.75	8.69	12.39	10.66	13.84	12.06	11.72	11.74	7.50	8.67	13.20	9.65	9.27	9.81	11.65	10.81	9.07	9.52	12.20	9.34	9.18	12.66	11.78	9.38	10.20	10.14	11.48	9.85	9.95	10.05	9.23	9.59
YPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY(-.98)	9.38	8.01	8.75	10.02	10.07	6.67	8.02	9.73	7.57	8.78	7.90	8.53	9.87	5.90	8.14	10.97	8.45	13.32	10.64	9.97	11.99	9.20	5.86	11.34	7.80	8.94	8.16	8.50	10.72	11.73	9.55	11.52	3.94	9.36	12.38	12.63	10.07	9.07	8.26	12.70	6.72	12.43	8.51	10.90	7.64
AADQDLGPEAPPEGVLGA	10.65	9.50	8.17	10.92	10.16	8.45	6.26	10.04	9.07	9.54	9.07	7.00	11.23	6.08	7.29	11.02	9.80	10.59	7.65	10.42	12.71	8.08	8.38	11.06	8.73	9.21	4.74	12.06	11.49	11.56	4.10	12.07	5.13	6.81	11.94	12.85	9.69	9.67	8.22	11.65	4.33	10.91	9.14	10.70	9.10
AADQDLGPEAPPEGVLGAL	11.25	7.33	6.80	11.59	11.90	10.08	6.09	11.79	3.69	10.16	8.56	9.98	11.04	8.22	8.42	12.86	11.05	11.80	9.52	12.00	12.63	9.72	6.97	12.45	10.84	10.50	6.19	12.74	11.51	9.60	9.80	12.48	5.92	8.06	12.13	12.53	10.73	9.95	9.13	11.74	9.79	11.29	6.73	10.80	10.79
AADQDLGPEAPPEGVLGALL	10.38	8.83	6.36	11.21	11.15	9.60	5.62	11.32	8.73	10.78	7.54	6.63	9.84	8.29	1.34	9.97	8.98	11.74	9.88	11.40	11.36	6.58	9.89	11.90	8.13	7.92	8.24	13.35	11.90	12.05	5.23	11.85	8.54	2.92	11.44	12.15	9.80	9.52	7.84	11.89	7.58	11.44	10.83	11.79	9.55
AADQDLGPEAPPEGVLGALLRV	10.47	8.48	1.23	11.47	11.22	9.54	7.97	11.73	9.01	10.31	6.58	6.10	11.34	7.61	7.91	11.61	9.62	12.10	9.72	11.99	11.94	5.46	9.82	12.34	9.24	9.01	7.62	13.11	11.93	11.89	8.58	12.17	8.37	8.01	11.93	11.74	9.51	9.08	6.75	11.90	4.32	10.97	10.47	10.97	8.98
LENPQPQAPA	10.48	8.82	5.06	10.22	10.04	8.37	4.67	10.50	8.04	9.16	8.45	7.49	10.50	7.46	4.95	11.03	9.39	10.28	8.10	9.67	10.78	2.88	8.09	10.27	8.33	9.43	8.03	11.69	11.09	11.09	7.04	12.05	1.44	5.33	12.02	12.76	9.85	9.71	9.00	12.38	7.01	11.09	8.37	11.10	8.78
LENPQPQAPARRLLPP	10.91	9.01	8.03	11.45	10.85	8.12	5.22	10.41	7.37	9.77	8.92	6.45	11.78	3.40	7.84	11.63	8.12	10.15	8.54	10.06	12.69	2.31	7.30	11.23	7.40	8.58	5.37	11.85	11.25	11.47	9.09	11.75	8.30	8.58	11.29	12.18	9.48	9.68	8.19	11.54	4.16	10.42	8.59	10.71	8.79
SLSAASPPMTEAGTPRRF	10.08	9.04	8.47	10.87	11.05	7.73	7.68	9.86	9.21	10.43	7.53	7.22	11.70	7.75	7.74	11.58	8.33	10.56	8.62	10.10	13.12	9.15	7.35	11.31	7.07	9.38	8.17	11.61	11.48	11.70	9.81	12.15	8.62	9.00	11.89	12.54	9.10	8.69	7.78	11.29	4.72	10.48	8.69	11.01	8.68
SPEPEAAAAVPRRL	11.11	10.05	7.58	7.14	10.70	8.61	7.81	10.14	9.10	10.80	2.97	8.08	10.59	7.96	7.81	10.66	7.38	9.66	9.97	10.25	11.07	10.06	9.68	10.74	8.10	11.52	9.62	11.30	8.08	10.53	10.11	11.09	6.43	9.95	8.22	11.71	9.76	10.92	8.56	10.65	9.23	12.34	12.41	11.90	12.95
SVPRGEAAGAVQELARALAHLLEAERQE	10.65	7.56	6.87	11.09	11.52	9.66	8.77	10.83	8.19	10.35	8.30	6.01	9.27	7.51	8.35	9.30	9.23	10.87	9.43	10.54	11.13	5.63	9.65	10.35	8.34	7.72	7.69	12.54	11.09	11.51	9.58	9.96	5.94	9.66	11.79	12.04	10.00	9.50	9.21	11.49	8.05	10.98	9.11	11.26	9.75
VKMALQQEGFD	10.48	8.61	5.95	10.30	10.53	8.62	5.09	9.18	8.80	9.33	8.74	8.40	10.34	8.28	9.00	10.74	9.14	9.30	7.33	8.70	11.78	9.78	7.57	10.33	9.21	8.62	8.55	11.14	10.74	10.61	7.87	11.16	8.84	9.05	11.15	11.58	9.65	9.65	9.42	10.87	8.53	9.88	9.15	9.85	9.70
YGGFLRKYP	10.89	9.74	8.11	11.35	11.77	8.30	6.70	11.24	7.11	10.92	9.43	5.62	11.09	5.25	7.91	12.16	7.53	10.61	9.85	9.79	12.43	8.73	6.03	12.14	7.86	6.61	7.62	12.61	12.00	11.69	4.78	12.40	8.41	3.00	12.21	13.03	9.67	9.63	8.06	11.98	8.57	10.98	8.90	10.78	9.18
YGGFLRKYPK	11.65	9.52	8.84	11.46	10.62	7.78	8.27	9.95	8.88	8.73	9.17	4.68	10.51	7.09	9.10	10.67	9.08	10.47	8.14	9.29	11.17	8.89	8.56	11.10	7.06	9.52	5.34	11.53	11.27	10.67	8.75	11.66	5.63	8.44	11.66	12.20	10.07	8.95	9.76	11.80	6.03	10.42	8.40	9.78	9.18
GGFMRGL	10.51	8.99	7.52	12.98	10.81	5.87	7.00	10.41	7.80	3.93	9.55	9.54	12.27	6.64	8.68	11.98	2.46	9.79	5.85	10.50	12.98	9.49	8.70	11.57	8.33	9.71	7.96	12.90	11.28	11.84	4.21	9.87	7.18	8.99	11.45	9.58	9.40	7.95	9.59	9.48	9.44	7.84	9.04	11.65	10.20
LEDEAKELQ	12.44	10.77	8.31	12.76	9.34	4.50	9.10	11.21	8.22	2.96	9.45	9.01	10.95	5.99	8.92	10.96	8.58	8.04	6.03	9.21	9.26	8.01	7.95	10.66	7.64	9.55	6.61	11.82	11.86	11.05	9.16	9.15	5.60	7.14	9.80	11.10	10.19	8.17	9.72	10.52	6.93	7.49	8.73	10.53	5.70
MDELYPVEPEEEANGGEVL	10.53	9.74	8.38	12.35	10.25	8.48	4.30	9.42	8.90	10.73	6.54	9.51	12.02	8.36	9.27	11.82	8.87	11.29	8.94	11.42	11.99	8.94	9.59	12.65	3.89	2.77	7.96	13.85	12.89	13.24	9.41	12.49	8.98	9.32	12.38	13.81	9.61	10.34	7.71	11.51	9.31	13.34	10.26	11.59	9.26
MDELYPVEPEEEANGGEVLA	10.52	9.26	7.70	13.49	9.56	9.13	7.30	10.38	9.35	10.67	3.66	9.86	12.48	6.52	3.37	12.11	6.34	11.24	7.69	10.62	12.13	9.48	9.48	12.26	7.66	9.61	8.64	13.48	12.14	12.47	5.52	11.83	8.26	5.39	11.32	12.84	9.06	9.42	9.22	10.54	9.21	13.25	6.30	11.43	9.01
SPQLEDEAKEL	9.82	8.76	8.50	9.67	10.92	8.02	6.99	9.31	8.11	9.57	5.75	9.25	10.16	7.03	6.90	10.92	8.61	9.17	9.31	9.87	11.61	8.60	5.55	10.21	7.58	2.84	7.94	11.52	10.49	11.07	6.01	11.18	7.37	6.72	11.05	12.57	9.21	9.64	8.99	10.71	8.81	10.99	9.31	10.00	9.07
SPQLEDEAKELQ	9.57	9.17	7.99	11.48	10.24	8.42	8.36	9.99	6.94	9.77	6.98	4.63	11.07	5.01	8.68	11.28	5.43	9.63	7.54	9.58	12.02	4.51	6.56	11.28	8.62	4.20	7.66	12.19	11.70	11.70	4.32	11.77	8.56	9.20	11.72	12.65	8.51	0.95	8.42	11.10	5.03	11.31	7.87	10.68	8.47
VGRPEWWMDYQ	10.62	7.60	8.18	11.49	10.16	6.55	8.70	10.21	5.90	10.03	9.07	6.51	11.10	8.97	5.12	11.11	10.08	9.44	8.51	10.43	11.76	8.94	8.28	12.14	8.11	8.18	8.03	13.07	10.79	12.05	4.93	11.79	8.14	9.06	10.82	12.68	5.78	9.61	7.29	10.47	7.08	11.51	6.11	10.39	8.33
YGGFMRF	11.68	9.68	9.05	11.62	10.88	8.45	7.64	10.31	8.00	8.98	7.87	8.16	10.80	7.96	8.41	11.84	9.68	9.65	8.23	10.28	11.90	9.16	7.33	11.83	9.20	9.30	7.86	12.43	7.26	12.00	6.60	12.41	8.19	8.04	12.19	13.63	10.58	10.42	9.72	11.98	7.10	9.56	6.62	8.34	7.95
YGGFMRGL	10.84	9.06	5.00	11.48	10.86	8.66	6.60	9.40	5.07	9.34	8.14	8.60	10.33	7.68	7.38	11.37	8.21	8.96	7.65	9.66	11.66	6.93	7.57	11.76	8.53	8.88	8.44	12.64	11.73	12.15	7.93	11.93	7.18	6.76	11.32	13.26	9.43	10.99	8.93	10.34	7.44	10.50	8.13	9.10	10.18
A(+42.01)AYKLVLIRH	9.64	10.53	9.50	6.16	7.84	8.09	9.66	6.55	9.61	8.92	7.70	10.92	9.13	10.47	10.58	11.01	9.47	8.84	9.47	9.30	9.72	11.09	9.47	9.60	9.67	8.87	10.91	10.87	7.21	9.71	11.38	8.47	9.35	11.34	7.76	10.48	12.08	11.47	10.35	10.05	10.16	9.63	10.17	9.46	10.32
A(+42.01)AYKLVLIRHG	9.71	10.63	9.61	9.92	11.17	9.57	9.47	7.09	7.06	9.92	9.80	10.60	9.54	10.21	10.36	10.55	10.18	8.63	9.16	9.12	9.79	11.21	8.84	10.95	8.89	10.39	10.73	10.93	6.86	9.56	10.31	8.13	10.54	11.35	8.42	10.72	12.03	11.68	10.61	9.16	9.88	10.51	9.84	10.57	11.53
A(+42.01)AYKLVLIRHGE	9.74	9.74	9.48	9.04	10.04	9.22	9.59	5.88	9.11	9.34	9.49	9.65	9.14	10.19	10.50	9.90	10.80	7.52	9.48	8.33	9.13	10.84	9.38	9.93	10.29	9.90	11.21	9.81	9.86	8.44	11.28	8.45	9.97	11.02	5.97	9.95	11.96	11.51	10.87	9.27	10.33	8.72	9.31	9.27	10.85
TYNFAVLKLMG	6.22	9.60	13.94	9.73	9.98	10.22	12.49	10.27	8.78	9.98	8.00	11.07	10.54	12.26	9.78	7.70	12.93	5.34	10.59	10.23	11.91	12.24	11.64	6.90	12.25	12.12	12.27	6.64	9.78	7.06	12.28	6.00	9.07	12.22	4.17	6.18	5.77	8.53	9.63	7.17	11.58	9.09	9.68	9.53	8.48
TYNFAVLKLMGRG	4.24	4.32	12.61	7.34	6.02	8.67	11.56	9.46	5.01	8.58	8.32	9.88	4.05	11.61	8.29	7.01	12.14	4.48	10.06	5.02	10.42	9.91	10.25	2.86	11.46	12.21	10.03	5.20	8.32	0.38	10.42	4.35	5.59	11.79	1.18	4.73	4.53	7.78	9.23	4.79	11.18	0.75	8.32	1.66	9.65
TYNFAVLKLMGRGTKF	7.63	9.83	9.62	8.98	9.97	9.71	9.50	4.23	7.71	11.06	8.75	10.40	7.52	10.24	9.50	10.89	11.49	8.31	12.12	5.78	6.89	10.54	10.21	9.61	10.14	12.44	9.87	5.96	9.47	9.62	10.11	10.13	9.69	11.17	6.37	8.57	9.97	10.15	12.20	10.31	8.64	7.62	10.17	6.89	9.99
EIGDEENSAKFPI(-.98)	9.98	8.74	10.27	11.21	10.48	7.86	8.55	9.44	8.08	9.01	7.87	5.58	11.49	8.58	9.02	10.61	8.91	9.05	8.15	9.72	12.38	9.16	8.40	10.83	8.59	8.90	5.90	10.90	11.05	10.67	8.71	11.42	4.08	7.89	11.97	11.95	10.08	9.59	8.97	10.95	8.00	10.73	9.11	12.11	10.03
SFFAVMGA	9.83	4.42	12.69	8.32	6.77	9.38	11.72	9.68	8.31	9.56	6.17	6.70	8.70	12.84	9.80	6.11	12.29	10.92	10.21	9.67	10.70	10.32	10.08	0.76	11.53	7.45	11.97	6.24	8.79	6.00	11.29	5.01	9.83	11.88	4.19	5.88	6.59	7.08	7.64	7.60	11.15	10.61	10.69	10.58	10.31
MQIFVKTL	13.24	10.76	9.56	11.28	10.78	9.29	8.84	11.37	7.31	7.52	10.36	10.81	10.28	8.92	10.32	10.15	9.60	8.90	8.72	8.93	9.64	10.35	8.05	11.00	9.58	9.12	7.91	10.78	6.27	9.96	8.81	9.97	5.90	10.75	7.57	9.30	11.46	10.91	9.58	10.30	8.30	8.94	8.71	8.73	10.60
MQIFVKTLT	12.17	10.00	7.45	9.55	10.83	6.51	8.02	10.96	8.86	8.18	9.86	10.64	11.01	8.74	10.43	10.20	9.36	9.07	7.89	8.36	10.92	10.46	9.23	12.45	11.09	10.74	10.96	11.92	8.14	10.05	11.07	10.04	10.20	10.28	10.44	11.23	11.42	10.34	7.66	10.94	10.22	6.76	9.66	6.74	10.09
MQIFVKTLTGK	12.20	10.68	7.70	7.13	9.42	8.01	7.65	11.38	6.68	7.30	8.68	10.61	10.51	7.88	5.47	9.97	7.68	8.80	9.42	7.74	10.14	9.83	7.03	12.14	8.60	11.37	8.69	12.26	8.48	10.71	7.20	9.13	8.49	8.58	7.92	10.76	12.15	11.72	7.87	10.39	6.56	9.77	9.81	8.05	11.87
STLHLVLRLRGG	12.86	10.26	9.83	8.86	9.00	9.36	10.22	11.43	10.11	9.54	10.91	10.68	10.90	8.24	11.12	8.66	8.73	9.54	10.06	9.30	9.68	10.27	9.49	10.91	10.66	11.25	10.01	10.46	9.59	9.56	9.93	9.84	9.54	9.66	10.05	9.32	10.36	10.30	11.35	8.97	9.69	9.14	10.35	9.63	11.23
TLHLVLRLRGG	13.94	7.23	7.54	8.50	8.37	9.95	11.12	10.76	7.79	9.38	11.83	10.60	11.29	8.62	11.95	8.77	8.99	9.34	8.77	9.39	9.90	10.52	9.95	10.26	10.81	11.09	9.65	9.47	9.30	9.05	9.96	9.04	10.06	9.89	6.70	9.13	10.28	9.37	11.34	9.40	10.61	8.36	10.31	9.23	11.46
AFVLVLYDELKKVI	10.01	10.81	11.86	8.12	12.30	11.51	11.59	5.74	9.87	11.09	12.15	10.88	5.56	12.27	11.32	10.46	13.11	10.29	13.15	11.12	12.42	9.12	11.60	9.89	12.30	6.07	11.18	9.14	11.44	11.16	13.20	7.78	13.06	14.58	10.24	9.20	10.81	10.77	8.96	11.83	11.53	11.22	14.54	11.23	10.36
GAFVLVLYDELKKVI	10.18	10.85	11.77	10.18	12.14	11.99	11.49	6.85	10.02	11.89	5.05	7.60	10.56	12.22	7.58	10.24	13.05	9.88	12.84	10.37	12.80	10.06	10.91	10.34	12.04	10.66	11.15	9.38	11.60	11.57	13.69	9.62	13.30	15.43	10.42	10.32	9.87	11.59	10.60	12.41	11.98	10.20	14.73	9.27	6.82
M(+42.01)DVFMKGL	12.44	9.24	10.44	5.92	10.10	10.92	10.52	10.25	10.91	9.50	8.25	11.22	10.01	10.52	10.60	9.86	9.82	9.16	9.03	10.54	7.33	12.28	11.10	10.17	10.44	10.82	12.50	9.81	5.00	8.83	12.27	8.37	11.99	11.67	1.81	7.79	11.37	11.57	11.22	8.13	11.08	7.45	11.82	8.43	12.51
SHLGGAVF	10.98	6.93	10.31	4.74	10.04	7.90	10.97	3.86	9.27	7.34	8.00	11.30	9.02	10.81	10.73	6.74	9.71	7.68	5.59	6.82	7.19	11.53	9.29	5.77	9.53	11.07	11.30	9.24	8.77	8.32	10.09	7.07	10.35	8.28	3.19	4.18	10.40	8.55	10.75	5.11	10.87	9.87	8.61	6.74	11.14
APIGLKAVVG	9.43	9.78	10.33	9.81	10.96	9.36	10.54	7.03	9.28	8.78	9.30	9.21	10.02	9.09	9.23	9.98	10.87	8.73	8.66	8.17	9.72	11.33	9.15	10.27	9.56	9.87	10.03	10.77	10.14	9.29	11.19	9.84	10.05	11.72	10.44	11.70	12.14	11.40	9.51	11.13	10.12	10.01	9.89	9.10	10.27
ALNSVAYERNAMQNY	11.02	8.17	6.74	12.06	12.26	9.11	7.26	9.59	8.96	10.06	10.11	7.78	11.40	7.25	8.79	11.69	6.25	7.61	7.55	9.90	11.09	10.02	6.53	12.02	8.38	9.56	7.92	11.97	10.87	11.77	9.34	11.56	5.02	7.41	10.03	11.96	8.82	9.03	7.60	11.31	7.42	9.85	6.64	10.66	5.53
ALNSVAYERNAMQNYE	10.86	8.32	4.31	11.78	11.14	8.23	6.84	9.21	8.28	10.30	6.22	7.11	11.97	7.16	7.80	11.88	8.90	9.08	7.18	9.95	12.66	4.64	8.21	11.64	3.50	7.84	6.62	11.99	11.41	11.95	5.43	11.82	5.34	4.19	10.59	12.16	8.56	9.66	9.23	11.58	5.55	10.34	8.44	11.00	9.24
RPKPQQFFGLM(-.98)	10.97	7.99	6.89	11.14	10.94	7.76	7.47	10.22	8.26	8.97	9.65	8.98	10.94	8.25	9.02	11.97	9.86	9.19	8.11	9.80	12.10	8.23	7.76	11.38	9.74	10.55	8.10	11.71	10.33	11.44	9.35	10.71	7.29	9.87	10.79	11.25	9.87	9.69	9.98	10.47	7.63	8.15	7.34	9.20	8.98
S(+42.01)DKPDMAEIEKFDK	12.95	9.89	8.77	8.74	9.14	8.34	9.06	11.01	8.28	9.42	10.59	9.53	11.72	6.41	9.85	10.29	8.54	9.37	8.93	9.40	10.60	9.75	9.36	11.00	8.93	10.58	9.00	11.09	8.12	10.21	9.41	10.26	9.70	6.48	8.09	10.83	11.51	11.37	10.97	10.78	8.14	9.84	9.91	11.07	12.13
GASLKPEFVDIINAKQ	11.74	11.37	6.40	8.55	12.25	9.45	8.40	7.53	9.53	9.07	10.17	11.32	9.66	8.34	9.60	10.63	9.33	8.30	9.29	5.58	10.56	10.11	10.42	12.54	9.75	10.71	9.90	11.84	10.47	11.29	9.89	10.96	10.24	6.78	10.38	12.65	13.09	11.64	11.33	11.29	10.57	6.33	12.04	10.01	12.49
SLKPEFVDIINAKQ	11.17	10.20	8.44	6.57	10.82	9.82	9.51	7.54	8.94	9.62	8.46	7.78	10.32	9.16	9.39	9.67	9.79	8.56	9.43	9.29	9.42	8.25	9.71	10.56	9.86	11.26	11.00	10.04	7.50	9.52	10.77	9.43	9.20	9.17	6.93	10.62	12.21	11.95	11.31	9.71	10.30	9.15	10.87	8.74	12.47
ASWTREPLE	9.20	9.28	7.49	9.89	11.38	9.47	8.77	9.40	6.42	10.39	4.46	8.82	10.23	7.52	6.84	10.95	9.04	10.06	9.25	8.94	11.99	7.40	8.70	10.69	7.36	4.43	9.42	11.32	11.03	11.01	9.60	11.83	8.16	8.99	12.29	12.92	9.63	9.33	8.79	12.21	7.83	10.32	8.54	9.68	6.70
ASWTREPLEE	3.79	9.56	10.11	9.31	10.35	7.78	12.03	9.80	8.94	9.28	9.98	8.73	10.16	7.50	7.75	10.45	9.97	9.59	9.18	9.18	11.58	6.42	7.36	10.08	6.80	9.52	9.77	10.80	10.36	10.55	6.42	11.00	6.31	9.81	11.48	12.25	7.57	9.03	8.87	11.78	8.87	9.77	7.59	9.35	7.46
EDEAAWSLDRTQQ	9.92	8.95	8.58	9.24	10.48	7.23	7.29	9.71	7.63	9.40	8.75	8.59	11.18	7.71	8.51	9.91	8.69	10.37	8.51	9.87	12.50	5.81	7.72	10.97	7.86	4.46	8.05	11.19	11.05	10.99	9.23	11.79	8.40	5.99	12.50	13.00	8.98	8.13	8.03	12.28	6.30	10.55	8.03	10.33	7.13
FLVFHSFGGG	9.15	7.66	8.94	8.58	10.14	8.19	6.74	10.47	6.13	10.76	10.46	10.05	5.37	10.03	9.27	10.84	12.03	6.00	12.39	5.96	11.07	11.41	7.18	10.27	7.47	11.04	12.17	8.73	10.29	9.66	11.71	8.95	5.88	9.04	6.45	7.21	7.33	11.24	9.53	9.10	9.57	8.05	11.15	7.69	9.76
GLQGFLVFH	9.46	9.70	12.11	3.49	9.33	10.01	10.85	5.31	9.07	9.17	5.79	11.14	8.46	11.43	9.94	7.77	11.16	6.38	9.46	9.54	10.04	10.48	9.47	5.79	10.20	9.84	10.47	4.26	8.43	6.90	11.16	6.37	10.28	11.48	9.64	5.44	8.85	9.77	9.75	5.28	10.82	4.22	9.99	6.03	9.72
LQGFLVFH	6.60	5.95	11.58	7.64	8.35	8.87	10.78	4.32	8.72	8.68	4.96	8.54	4.68	10.49	9.06	7.40	10.88	2.65	9.62	4.52	4.31	8.38	9.42	4.97	9.71	8.87	11.31	5.48	8.39	3.57	11.91	6.21	10.72	10.85	2.67	6.88	8.74	9.58	8.92	7.66	11.54	4.85	9.83	5.19	8.97
SGFTSLLMERL	9.07	7.88	10.60	7.93	6.68	8.16	10.60	2.18	9.62	9.31	3.08	9.05	2.94	11.41	9.36	8.22	12.46	6.92	11.35	10.16	11.65	8.74	10.14	8.81	11.32	10.25	10.38	8.38	9.70	8.26	11.58	5.16	10.11	13.99	11.38	8.50	10.60	11.44	10.46	9.89	9.77	7.54	13.11	10.23	10.49
SIYPAPQVS	7.12	7.17	11.85	4.81	8.22	9.26	12.06	2.69	6.51	8.46	7.66	8.87	7.06	11.66	8.66	5.06	10.92	10.98	8.81	1.34	10.74	11.08	10.17	5.42	10.65	10.11	11.86	3.66	8.43	6.72	12.18	6.04	11.50	11.48	2.88	6.38	9.66	10.66	10.52	7.85	12.06	3.97	9.03	3.31	7.07
TGLQGFLVFH	4.10	3.90	12.49	3.77	8.34	8.72	11.82	1.72	8.94	9.24	5.45	7.69	3.83	12.18	8.98	2.22	11.62	3.22	9.17	-0.77	0.35	10.49	10.25	0.21	11.18	8.11	12.06	2.89	7.95	5.80	11.94	5.00	10.98	11.08	9.61	2.41	6.35	7.60	8.92	6.22	11.12	0.81	8.61	2.48	7.23
TGLQGFLVFHSFGGG	3.34	9.84	11.41	9.04	8.96	9.48	11.46	10.11	10.28	11.35	7.54	8.11	9.85	12.46	7.49	3.88	13.30	5.66	11.44	7.03	11.12	7.27	11.02	7.43	10.91	9.43	11.45	7.29	9.48	7.58	12.23	6.34	11.42	13.28	11.79	6.96	7.17	10.88	10.91	7.84	11.57	10.01	11.96	10.28	7.78
TSLLMERL	6.19	5.31	12.68	6.64	7.18	8.00	11.75	2.68	8.85	7.92	5.07	9.28	5.78	11.70	4.68	7.12	10.57	4.65	9.85	4.68	4.90	10.46	9.52	5.53	10.00	9.30	10.63	6.73	2.93	5.01	11.73	-0.43	10.73	11.53	5.19	6.59	9.46	8.00	7.53	5.01	9.42	5.34	6.38	4.22	4.53
SGPFGQIFRPDNFVFGQ	5.72	4.90	12.81	8.60	9.84	11.52	12.97	9.74	10.41	10.19	5.38	10.26	9.66	13.75	6.57	5.88	13.46	6.02	11.90	6.83	12.46	11.15	12.22	8.55	11.96	5.95	12.76	7.92	8.47	8.31	11.74	7.68	11.00	13.01	11.13	6.68	7.08	9.96	9.91	7.49	10.18	8.18	12.19	8.98	8.67

EigenMS normalization

After imputation using knn (k = 7), the data was normalized using EigenMS to account for sample-to-sample variability.

EigenMS normalization preserves the treatment group differences in the data by estimating treatment effects with an ANOVA model, then uses singular value decomposition on the model residual matrix to identify and remove the bias.

Code

plot_grid(hist_eigenms, qq_eigenms, pca_eigenms, nrow = 1)

Code

norm_d1_mod = norm_d1[-1,] %>%
        as.data.frame() %>%
        rownames_to_column(., var = "rowname") %>%
        mutate(across(-rowname, as.numeric)) %>%
        column_to_rownames(., var = "rowname")
#write.csv(norm_d1_mod, file = "after_norm_data.csv")

#rownames(norm_d1_mod) == feature_name$variable
rownames(norm_d1_mod) = feature_name$name

# display table
norm_d1_mod %>% 
        mutate(across(everything(), round, digit=2)) %>%
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

	Hypo_39	Hypo_36	Hypo_44	Hypo_25	Hypo_48	Hypo_52	Hypo_21	Hypo_20	Hypo_55	Hypo_60	Hypo_19	Hypo_42	Hypo_37	Hypo_24	Hypo_22	Hypo_43	Hypo_35	Hypo_63	Hypo_66	Hypo_54	Hypo_65	Hypo_49	Hypo_53	Hypo_23	Hypo_31	Hypo_45	Hypo_32	Hypo_57	Hypo_33	Hypo_40	Hypo_47	Hypo_58	Hypo_51	Hypo_46	Hypo_64	Hypo_59	Hypo_27	Hypo_34	Hypo_26	Hypo_61	Hypo_38	Hypo_62	Hypo_50	Hypo_56	Hypo_41
A(+42.01)LLRGVFIVAAKR	9.63	9.97	10.50	11.57	11.77	10.33	9.91	8.39	10.38	7.56	8.97	10.13	9.47	9.25	10.69	10.59	8.49	7.73	7.39	7.67	4.59	9.55	8.83	9.66	9.89	10.84	9.84	9.11	11.17	8.43	11.27	8.81	10.58	11.48	11.12	8.90	10.82	9.98	10.42	8.02	9.54	6.77	9.24	9.64	11.06
SAMLIQKL	9.92	8.72	9.84	10.69	10.28	8.54	9.13	6.09	10.68	7.37	11.01	10.49	10.38	9.38	10.33	11.48	10.53	9.04	9.05	9.97	8.81	10.33	9.60	9.53	9.85	7.58	10.65	10.29	8.35	10.18	11.85	9.56	8.39	10.56	10.76	9.50	9.58	9.54	9.50	8.63	9.02	8.97	9.01	9.28	10.38
TDYLMKIL	6.88	5.28	10.06	8.78	8.63	7.01	9.41	11.64	6.57	2.76	3.87	8.20	6.54	8.89	8.84	9.73	7.46	3.74	4.58	5.67	6.34	9.77	2.80	7.42	9.02	7.94	8.11	9.11	5.59	5.61	10.29	6.21	8.55	9.72	10.35	3.79	8.82	8.72	8.57	2.47	8.04	9.98	8.84	11.67	9.71
PYQYPAL	9.68	9.82	11.01	6.39	10.87	8.84	9.72	10.01	9.15	6.37	9.64	9.25	9.45	9.65	9.87	11.15	8.45	6.87	6.04	10.04	6.96	10.15	8.40	9.44	9.23	10.44	9.26	5.71	11.39	8.43	10.54	8.26	9.10	10.62	4.67	7.51	9.86	9.05	9.36	7.28	8.66	5.58	8.29	9.09	10.82
SESLFVSNHAY	9.54	9.91	8.96	9.08	9.95	8.83	10.26	10.09	9.54	8.82	8.90	9.47	10.06	9.84	10.22	10.34	10.10	8.94	8.90	9.67	8.98	9.52	9.61	9.14	9.98	10.40	9.73	9.11	9.15	9.52	10.26	9.16	9.18	10.04	8.45	9.25	9.21	9.11	9.33	8.65	9.15	9.55	9.05	9.99	10.32
SLFVSNHAY	9.42	9.64	10.36	8.29	10.85	9.10	10.48	9.88	9.71	8.09	10.33	9.51	9.88	9.74	10.02	10.57	9.65	7.49	7.53	9.91	7.98	8.21	9.44	9.46	9.85	10.34	9.82	9.17	8.21	9.27	10.46	8.34	9.60	9.94	7.01	8.60	9.36	9.08	9.70	7.93	9.49	7.87	8.74	9.88	10.58
GAAAQSLYIANHAY	8.06	9.28	8.44	9.14	10.76	8.96	9.46	9.54	8.65	8.99	9.88	10.76	9.41	9.99	9.96	10.05	8.80	8.49	10.50	9.91	9.10	10.07	9.10	9.86	10.11	11.00	9.75	9.33	11.51	9.41	8.50	9.18	8.99	13.04	9.66	9.11	9.74	9.30	9.92	8.67	11.02	10.11	9.46	10.25	11.48
SLYIANHAY	9.20	9.50	8.88	9.07	11.22	9.92	10.20	9.67	9.95	9.30	10.87	9.73	9.98	8.58	10.22	10.52	9.75	7.66	8.58	9.83	8.00	7.81	9.36	9.21	9.33	9.49	9.73	9.06	7.97	9.11	10.31	8.37	9.60	9.99	7.00	8.49	9.28	9.06	9.53	8.74	9.62	7.65	8.65	9.41	9.93
DIDTAAKFIGAGAA	7.42	10.00	11.05	9.78	10.95	9.33	7.21	6.84	8.92	10.20	11.67	10.47	10.98	9.33	9.62	10.02	10.20	10.23	11.07	10.76	7.96	9.93	9.23	8.75	8.30	8.39	8.47	8.79	4.60	8.41	7.12	9.50	6.56	11.66	10.55	10.52	9.54	10.08	7.53	11.56	8.21	10.48	9.78	8.76	8.40
VPPVQVSPLIKL	11.29	8.46	11.13	9.85	9.53	8.99	9.72	10.78	8.24	9.58	10.92	9.42	9.57	10.38	10.19	9.97	8.13	7.29	11.17	8.24	9.74	9.12	8.01	10.21	10.25	10.10	9.95	10.21	11.00	9.57	10.18	8.62	8.40	10.54	8.34	8.61	9.31	10.48	9.67	9.09	10.21	9.06	9.21	9.48	10.59
VPPVQVSPLIKLGRY	11.32	10.41	9.84	8.19	10.22	9.79	10.85	10.62	9.35	9.04	10.63	9.56	9.10	11.47	10.92	10.72	9.63	7.73	7.92	9.02	8.57	8.86	10.22	10.07	11.44	11.93	8.12	9.51	10.74	8.66	10.71	8.34	9.81	11.58	10.50	8.76	10.68	9.79	10.93	9.25	8.34	8.81	7.78	8.63	9.08
TIDFPEFL	10.18	8.34	11.25	10.12	11.82	9.70	10.34	12.04	9.73	7.17	7.17	8.90	9.86	10.23	9.52	8.45	8.36	11.47	5.77	10.33	5.03	10.86	10.05	8.98	9.53	9.58	10.01	11.44	11.30	9.40	10.79	7.10	10.41	10.55	7.49	8.49	9.64	9.61	9.33	7.65	8.76	4.78	10.34	5.93	12.14
Q(-17.03)EDAELQP	10.27	8.28	7.08	9.48	5.97	9.23	8.34	8.12	8.37	11.41	5.46	6.01	10.11	9.58	10.73	7.60	9.79	12.06	10.49	8.08	12.26	8.46	7.12	8.61	9.31	7.95	8.68	8.86	8.49	9.00	7.30	11.98	8.80	6.50	12.96	11.92	7.28	8.06	9.24	11.37	8.11	11.76	7.76	8.24	7.48
Q(-17.03)EDAELQPR	8.92	7.65	9.65	9.51	6.93	7.35	8.38	7.91	8.01	10.18	6.45	9.11	9.34	8.39	7.74	7.20	9.75	11.09	9.09	8.67	11.37	10.20	8.93	7.90	8.02	6.36	9.75	9.07	9.12	8.51	9.90	11.40	3.70	5.77	12.56	11.63	8.03	7.90	7.49	11.93	11.03	11.25	9.77	8.91	10.11
SAVISLEGKPL	9.31	9.43	7.95	9.11	10.21	9.61	10.00	9.15	9.78	9.87	10.20	9.88	10.08	9.93	9.55	10.25	9.92	9.08	9.34	9.75	9.58	9.14	9.44	9.34	8.97	10.56	10.38	9.49	9.53	9.39	10.55	9.12	8.66	10.66	8.00	8.91	9.01	8.82	8.81	9.18	8.77	10.22	9.12	9.76	10.56
FLGEAYHHVPESQ	10.17	7.48	9.67	10.70	8.38	5.22	8.27	9.12	4.45	9.42	9.55	4.53	10.25	8.68	10.38	7.96	9.55	10.64	10.10	8.30	11.47	11.15	4.99	9.11	10.08	9.23	10.82	9.69	11.38	10.69	10.98	12.73	10.17	9.86	12.73	10.44	9.40	9.23	10.42	11.52	12.26	10.39	8.49	9.13	10.50
FLGEAYHHVPESQRD	9.28	7.58	9.81	9.53	8.49	7.33	8.92	7.75	5.88	10.28	8.23	7.39	9.95	9.40	9.09	8.29	10.47	10.24	9.41	8.07	10.98	10.32	8.54	9.13	8.76	9.00	10.20	8.51	9.90	9.55	3.97	10.94	7.18	3.90	11.73	9.99	9.32	8.82	8.93	11.62	11.56	9.74	9.15	7.31	6.63
LGVLFNPYYDPLQWKSSRFE	11.50	8.10	8.31	10.20	9.25	9.09	10.02	10.44	10.36	11.32	8.74	8.37	11.05	9.42	10.46	9.11	10.90	11.72	11.13	10.44	11.38	8.88	10.63	11.02	10.58	10.02	10.21	10.67	10.09	10.45	10.21	11.33	9.54	8.40	11.74	10.21	9.51	9.89	10.20	10.31	11.07	9.97	9.79	9.18	7.80
Q(-17.03)YDRVAELDQLLHY	11.13	8.68	7.96	11.37	9.40	9.73	10.10	10.55	10.00	11.36	8.63	9.07	11.15	9.97	9.78	9.66	10.51	12.28	11.39	11.09	11.25	10.47	10.98	11.15	10.35	9.94	11.28	11.22	10.87	9.81	10.49	11.51	10.14	9.91	11.76	10.53	9.32	9.67	9.96	11.42	10.89	10.53	10.46	9.39	9.96
SVLISLKQAPLVH	10.21	9.41	9.93	10.05	10.80	8.08	9.23	8.31	10.42	10.13	8.60	9.27	8.79	10.88	10.22	10.13	9.03	10.15	8.31	11.04	8.04	9.64	9.87	10.03	9.91	10.92	10.93	10.55	11.28	10.27	11.35	9.10	9.58	10.55	9.88	8.72	9.45	10.66	10.22	7.08	9.95	9.05	8.33	9.64	10.93
TTMIIDHVVPEPG	9.69	7.92	11.81	10.28	9.45	8.98	10.17	11.62	9.46	9.12	6.84	9.01	10.55	9.63	9.75	10.57	9.52	11.52	9.20	4.94	10.69	9.64	8.88	9.19	5.96	10.72	9.64	8.11	10.48	9.36	10.39	8.62	9.44	8.56	10.61	6.51	10.29	10.22	9.50	8.24	5.06	8.01	10.16	8.69	12.14
TVVYGEPITA	9.44	7.98	9.56	5.45	10.27	7.71	8.07	12.35	7.42	4.66	7.04	8.50	9.71	8.60	9.40	11.01	8.97	6.00	6.29	7.47	4.15	8.88	9.08	8.90	8.44	10.41	7.94	5.28	11.66	5.38	9.30	5.00	7.12	9.71	5.82	6.26	8.74	7.02	7.48	6.57	6.99	2.77	7.77	5.26	11.20
S(+42.01)ILKIHAREIFD	10.25	10.21	10.87	7.31	11.49	10.81	10.24	9.81	9.54	9.26	10.43	11.24	10.42	10.40	11.59	11.53	10.60	10.04	9.50	10.73	8.09	7.72	10.13	10.87	10.52	11.56	9.25	9.89	9.23	10.65	11.15	9.41	9.71	11.58	8.41	8.72	10.29	8.93	10.77	9.72	9.87	9.41	8.61	9.51	9.15
VKVGVNGFG	8.79	10.66	12.77	6.71	11.27	10.15	10.58	10.06	9.90	10.65	8.92	10.33	10.21	7.43	10.60	10.38	8.61	9.42	10.32	9.10	9.08	10.76	9.80	9.30	6.44	8.08	9.26	9.41	9.50	9.81	9.11	9.56	9.59	9.98	9.93	9.59	9.28	9.49	8.59	9.88	9.70	9.69	9.98	9.81	10.54
VKVGVNGFGR	8.83	9.92	10.24	10.52	10.45	9.31	10.68	9.35	10.92	9.68	11.12	10.80	9.68	11.06	11.44	10.10	10.85	10.05	8.55	10.19	9.80	9.27	9.90	10.53	10.43	11.12	9.42	10.88	9.94	10.47	10.43	10.72	10.94	9.71	10.37	10.91	9.82	11.23	10.34	11.18	10.89	8.85	10.00	9.51	10.31
VKVGVNGFGRIG	9.50	10.45	10.90	7.33	10.84	10.41	10.32	9.67	10.48	10.99	10.18	10.46	10.89	10.07	9.21	10.29	9.74	10.61	10.39	9.15	9.68	9.21	9.96	9.52	9.69	7.40	7.40	9.51	8.67	9.81	8.54	9.74	9.53	9.86	9.95	9.38	9.32	9.48	9.30	9.79	9.76	10.54	9.78	9.72	11.38
SGSAKVAFSAIRSTNH	10.17	6.53	5.20	9.76	8.72	9.08	9.25	8.69	9.30	9.63	8.83	9.26	9.52	9.37	3.47	8.90	8.82	10.48	9.48	7.92	10.93	10.37	9.84	9.37	6.09	5.37	10.50	8.24	9.64	9.55	10.74	10.99	10.05	10.07	11.29	10.83	9.43	7.74	9.13	10.73	10.87	9.92	4.05	8.42	9.05
A(+42.01)GQAFRKFLPLFDRVLVER	11.94	9.25	9.74	10.49	9.73	10.91	10.64	12.00	9.89	8.49	10.34	10.28	10.72	10.69	10.01	11.19	10.56	8.36	9.24	9.98	10.18	9.07	9.80	9.43	10.74	11.79	9.79	9.92	10.84	8.10	10.54	9.80	9.85	11.01	10.47	7.79	10.62	10.63	10.22	9.80	9.21	7.04	10.96	8.93	10.58
DILGKYVD	13.15	10.99	11.88	12.10	10.56	10.72	10.38	11.98	9.39	9.75	10.71	11.40	10.99	10.56	7.87	10.57	12.28	8.52	10.30	9.51	10.35	10.99	11.35	11.00	12.01	12.20	11.23	10.81	11.59	7.38	9.74	9.98	10.36	11.30	10.00	9.98	10.33	10.94	10.17	8.55	8.43	10.49	10.46	9.60	11.48
AEALERMFL	7.75	8.87	10.71	9.75	8.90	7.07	9.35	8.00	8.22	4.94	7.35	10.01	7.70	2.62	8.51	8.74	9.86	9.05	6.03	6.62	2.10	7.50	7.80	7.66	8.99	8.33	9.27	9.59	12.21	7.03	10.19	3.47	8.05	11.11	9.18	5.38	8.51	10.12	9.84	9.05	8.98	8.60	10.24	9.21	10.19
GAEALERMFL	7.34	9.51	11.36	9.07	10.14	8.40	7.67	10.37	9.22	8.06	8.33	9.75	8.65	9.40	8.59	8.08	7.65	9.66	3.85	8.99	10.14	9.09	8.23	7.72	8.92	9.44	8.51	9.74	5.44	8.79	9.79	4.47	7.94	9.96	5.37	7.52	7.85	8.98	9.27	5.94	7.90	4.22	9.27	8.82	9.25
PVNFKLL	8.02	7.92	9.32	7.03	8.66	6.70	8.19	9.16	8.64	4.69	8.20	9.45	8.72	9.82	9.64	8.67	6.50	2.67	4.99	7.96	4.59	11.22	7.05	7.83	9.55	10.49	7.34	8.51	11.39	8.82	10.86	5.37	9.46	10.01	9.43	6.51	9.61	8.88	9.24	8.88	8.60	3.13	6.00	7.69	8.04
SLDKFLA	7.95	7.27	9.58	7.92	9.85	7.39	8.24	7.61	8.79	5.49	9.19	10.04	10.15	8.36	8.72	10.64	8.31	2.82	4.27	7.70	3.85	8.22	8.11	5.39	8.99	8.72	8.20	8.15	7.25	9.57	9.34	6.18	7.33	8.35	0.94	5.56	7.05	7.99	8.93	5.34	7.97	3.95	8.00	8.42	9.28
SLDKFLASVSTVLTSKYR	7.53	10.69	9.79	11.03	10.03	10.48	7.03	11.62	9.36	8.59	8.28	12.09	8.19	10.78	9.16	8.52	8.26	9.17	9.60	9.26	6.66	9.67	8.43	9.99	9.10	8.62	7.71	9.23	10.35	10.04	8.93	6.61	10.45	11.01	6.69	8.79	9.84	10.46	10.10	5.14	11.66	9.27	11.57	10.24	9.55
SVSTVLTSKYR	7.98	9.69	9.65	8.19	9.93	9.29	9.14	11.02	8.80	9.86	8.97	12.66	8.30	5.78	8.03	7.97	8.67	7.44	7.75	7.80	7.42	6.31	8.39	8.93	8.58	10.58	8.65	8.77	8.86	9.14	10.83	7.91	10.47	9.77	7.29	9.57	10.14	8.79	8.06	7.98	10.58	8.46	9.18	9.36	5.11
TPAVHASLDKFLA	7.26	8.42	6.48	11.19	9.28	8.26	8.71	9.10	6.97	5.94	8.24	9.98	8.90	10.22	9.10	10.45	9.66	9.61	6.27	7.67	10.07	7.23	8.56	8.05	9.67	9.64	8.42	8.28	5.80	9.79	9.92	4.72	6.65	11.35	9.59	2.80	8.96	9.55	10.02	5.81	8.60	10.02	10.89	10.61	10.67
TPAVHASLDKFLASVSTVLTSKYR	8.57	11.71	10.85	11.76	10.14	9.80	9.51	12.25	8.95	11.12	8.58	12.53	7.84	8.40	9.35	8.30	7.83	7.52	10.75	9.00	7.20	9.16	9.72	10.58	8.22	8.19	9.49	9.26	9.01	7.75	10.15	7.17	9.86	8.31	10.03	7.99	10.48	10.47	9.12	9.49	9.12	7.09	10.13	9.56	9.78
TYFPHFDL	7.53	6.49	8.73	7.93	9.11	6.40	7.57	7.25	7.88	4.03	6.43	9.01	7.79	8.64	8.25	8.31	6.94	8.87	3.01	7.24	1.75	8.65	6.99	7.65	8.42	7.99	8.03	8.04	12.28	8.63	9.71	5.80	7.97	8.89	8.99	4.96	8.14	9.59	9.95	3.56	8.03	0.09	8.52	5.70	9.30
TYFPHFDLSHG	8.57	8.62	9.34	8.27	10.76	8.37	8.74	8.60	8.98	6.41	8.91	11.67	9.37	9.56	9.51	9.30	7.53	3.33	6.16	7.90	9.18	7.55	8.71	8.04	6.42	10.06	8.90	7.64	13.20	7.02	9.80	7.95	8.86	10.99	9.94	7.39	8.25	9.84	11.18	6.41	10.49	8.61	9.60	7.75	10.70
THYKLVPHQFAH	10.30	8.34	9.11	9.05	10.18	10.20	10.79	10.06	10.23	8.56	11.10	9.20	9.75	10.32	9.90	10.83	10.30	7.97	9.46	9.97	8.12	8.03	10.13	9.82	9.68	11.17	9.69	8.71	9.74	9.75	8.54	8.78	8.74	8.71	5.21	7.92	9.67	9.50	9.53	9.12	9.48	7.82	9.66	9.35	10.11
TAYAIYELAKA	10.51	10.51	8.85	10.07	8.91	8.58	9.27	8.78	9.72	7.45	9.28	10.54	10.55	9.52	9.95	10.91	9.95	6.19	5.69	9.23	7.34	8.73	9.42	8.83	9.93	10.12	8.89	7.90	11.31	6.87	10.56	8.51	8.57	11.63	10.62	2.65	10.51	10.31	11.18	10.59	9.28	4.02	9.35	11.20	11.22
TAYAIYELAKASFPKKQD	9.33	8.62	10.80	10.37	8.43	10.08	10.25	10.12	9.80	9.71	9.91	10.20	10.95	10.21	7.01	10.28	9.65	11.24	10.16	11.02	8.59	10.20	10.32	11.11	10.55	11.58	9.96	9.14	9.29	10.73	11.25	7.80	9.73	10.58	11.00	8.73	11.50	10.30	10.07	9.96	7.56	9.16	10.09	10.09	11.20
SGFAAPFFIVRHQLLKK	10.45	8.97	11.40	8.94	12.60	11.70	6.79	9.55	10.95	8.95	7.21	9.99	10.61	10.30	10.42	10.84	9.25	9.00	7.34	9.78	9.45	8.85	9.41	9.70	10.73	12.07	8.99	6.86	7.57	10.29	10.86	7.75	10.60	11.28	10.21	9.32	11.87	6.38	11.92	8.37	8.67	9.62	8.27	10.30	8.50
AFQKVVAGVANALSHKYH	8.93	10.74	10.71	9.56	10.57	8.39	9.14	9.97	9.01	8.35	8.97	12.28	8.35	9.33	5.64	10.10	10.12	11.18	10.39	10.79	8.84	9.34	9.37	10.29	9.74	10.09	8.73	10.53	9.60	6.72	10.73	5.33	9.50	10.84	7.28	9.94	9.20	9.97	10.76	4.82	10.16	8.88	6.40	9.76	9.53
KVVAGVANALSHKYH	9.10	11.40	10.99	10.41	10.73	10.01	10.01	11.12	9.42	5.84	8.92	12.49	8.70	9.05	9.83	9.88	10.54	8.31	9.50	8.90	7.77	9.59	9.51	9.23	9.47	10.06	9.76	9.13	9.19	9.48	7.87	8.38	9.72	8.65	4.88	9.59	9.50	10.05	11.23	8.08	10.54	9.04	9.73	9.58	6.47
TPEAQAAFQKVVAGVANALSHKYH	8.22	10.77	10.41	9.37	9.87	9.53	8.60	11.06	10.21	7.96	8.85	11.70	8.95	10.45	10.10	9.14	9.30	8.30	8.53	9.41	6.76	7.17	7.84	8.89	9.35	10.38	9.50	9.09	9.31	9.54	9.09	7.59	7.37	10.83	5.92	7.94	9.38	9.74	11.09	6.52	10.12	8.55	10.83	10.17	9.48
RTLYGFGG	9.52	9.83	11.36	10.15	10.61	9.92	10.46	10.41	9.61	8.73	9.13	10.08	9.70	8.29	9.41	9.55	9.96	8.52	9.05	8.71	9.82	9.45	8.61	9.24	9.31	9.74	9.17	8.97	8.80	9.35	9.64	9.17	9.88	10.27	10.55	10.29	9.83	10.24	9.33	9.64	10.70	9.92	9.22	9.91	10.94
TLYGFGG	10.10	9.02	10.03	11.17	9.51	9.33	9.90	10.36	9.26	7.66	9.77	9.53	8.84	10.49	9.74	10.37	9.22	7.10	7.65	7.38	9.77	10.49	8.99	9.52	9.25	9.98	9.88	10.38	9.67	9.40	11.67	8.39	10.02	9.31	9.19	8.45	9.73	9.66	9.77	9.12	9.93	7.83	8.73	9.60	10.47
TLSKIFKLGGKDSRSGSPMARR	9.92	9.76	11.14	11.84	9.86	9.08	9.78	9.29	8.79	9.52	9.15	11.98	8.73	9.93	8.89	10.14	10.81	7.62	10.16	10.73	7.30	10.81	9.43	11.10	9.84	12.36	9.99	10.21	10.17	11.13	10.96	7.25	9.46	10.64	10.87	7.86	11.10	10.46	10.09	10.38	10.56	7.78	6.73	10.52	11.42
SIGRFFG	8.88	7.14	10.31	7.75	10.02	6.69	9.79	7.90	6.95	4.74	9.41	8.49	7.64	8.30	9.23	11.11	9.23	2.04	4.65	9.00	10.37	8.87	8.34	8.39	9.41	10.42	7.99	9.41	7.52	7.79	9.84	4.11	7.53	9.38	8.55	5.08	7.90	8.63	8.16	3.95	6.91	8.55	7.07	3.66	10.85
SIGRFFGG	8.85	6.39	10.23	7.03	7.57	7.59	9.50	7.22	5.47	3.12	8.31	8.30	7.31	8.93	8.81	9.88	8.69	0.84	2.47	5.95	5.09	8.57	8.41	7.91	9.41	10.46	7.80	8.50	12.59	7.77	10.49	6.25	8.06	8.48	2.18	4.04	8.14	9.13	7.92	1.17	7.73	8.78	6.68	8.19	11.30
SIGRFFGGDRG	11.10	7.48	8.82	8.88	7.93	8.24	9.50	7.75	8.59	7.13	10.72	10.44	9.64	9.53	9.39	10.27	10.25	4.66	7.26	10.30	8.30	8.54	9.60	8.72	10.01	9.75	7.01	8.92	10.50	7.19	9.66	7.63	7.18	9.75	7.40	4.90	9.07	10.34	10.23	7.04	8.01	4.45	8.14	8.56	8.77
PMFVVNTNVPRA	9.09	9.40	10.70	6.66	10.64	9.82	10.12	9.97	10.33	9.48	9.80	8.82	10.29	8.55	9.98	10.84	10.05	8.38	7.90	10.70	8.79	6.60	9.18	9.69	10.83	10.58	10.03	9.68	5.59	9.84	10.31	10.04	9.34	11.65	11.80	9.18	9.18	8.95	9.52	9.32	9.99	10.17	9.01	10.23	10.22
SSPETLISDLLMRESTENVPRTRLEDPSMW	7.40	8.14	9.82	9.43	10.73	9.26	10.15	9.86	9.63	11.20	9.58	10.06	10.87	6.24	9.42	11.05	11.08	14.27	12.81	10.88	11.40	8.59	9.09	12.28	10.03	9.76	10.91	10.36	9.67	8.09	10.01	11.89	10.22	9.53	12.53	11.02	9.11	10.13	10.52	11.15	11.11	10.06	10.19	8.21	9.82
YPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY(-.98)	9.22	7.11	9.63	8.96	8.53	7.01	9.14	8.43	8.20	9.77	7.91	9.02	9.18	7.04	8.97	8.97	9.59	13.69	12.01	8.70	11.66	10.55	6.60	9.86	8.55	9.33	9.93	6.45	9.32	10.37	10.48	10.92	5.27	10.22	12.16	11.51	9.53	8.95	8.65	12.34	8.54	12.34	8.91	9.44	7.61
AADQDLGPEAPPEGVLGA	10.18	8.01	9.80	9.30	7.69	9.06	8.23	7.89	10.10	11.20	9.02	7.66	10.06	8.11	8.59	7.75	11.83	11.12	9.99	8.37	12.22	10.19	9.62	8.58	10.03	9.72	7.68	8.63	9.35	9.38	5.70	11.05	7.33	8.34	11.61	10.97	8.67	9.38	8.76	11.06	7.28	10.70	9.80	8.32	8.89
AADQDLGPEAPPEGVLGAL	10.41	6.14	8.55	10.78	10.04	10.66	7.90	10.26	4.56	11.47	8.63	10.24	10.10	10.07	9.36	10.36	12.84	12.19	11.43	10.59	12.30	11.16	8.04	10.32	11.96	10.69	8.47	9.84	10.27	8.00	11.12	11.69	7.65	9.44	12.04	10.87	9.43	9.27	9.25	11.22	12.04	11.06	7.10	9.06	10.26
AADQDLGPEAPPEGVLGALL	10.28	7.36	7.92	10.03	8.38	10.07	7.31	9.81	9.97	12.18	8.37	7.76	8.95	9.81	2.98	6.85	10.27	12.73	11.76	9.70	10.63	8.84	11.02	9.43	9.19	8.79	10.82	9.97	9.80	9.89	6.48	11.11	10.65	3.98	11.37	10.07	8.48	8.74	8.32	11.05	10.51	11.62	10.96	9.54	9.56
AADQDLGPEAPPEGVLGALLRV	10.52	6.96	2.75	10.21	8.29	9.98	9.62	10.23	10.32	11.71	7.55	7.40	10.46	9.05	9.67	8.38	10.80	13.20	11.58	10.24	11.13	7.88	10.96	9.83	10.27	10.01	10.25	9.66	9.66	9.64	9.81	11.45	10.53	9.01	11.86	9.60	8.19	8.29	7.29	11.00	7.37	11.23	10.55	8.63	9.10
LENPQPQAPA	9.92	7.25	7.04	9.09	7.30	8.98	6.73	8.76	9.29	10.73	9.04	8.33	9.44	9.44	6.49	7.73	11.17	11.12	10.31	7.87	10.15	5.05	9.38	7.55	9.60	10.06	10.87	7.98	9.15	8.89	8.54	11.17	3.69	6.75	11.96	10.53	8.26	8.79	9.33	11.57	10.06	11.09	8.63	8.76	8.46
LENPQPQAPARRLLPP	10.76	7.38	9.59	9.68	7.96	8.68	7.14	8.27	8.58	11.46	9.22	7.51	10.63	5.29	9.47	8.07	9.93	10.96	10.87	7.87	12.01	4.81	8.59	8.57	8.67	9.40	8.46	8.18	8.73	9.03	10.66	10.75	10.68	9.98	10.98	10.09	8.42	9.32	8.88	10.79	7.43	10.39	9.13	8.10	8.83
SLSAASPPMTEAGTPRRF	10.31	7.91	9.31	9.51	8.90	8.03	8.82	8.45	10.08	11.54	7.93	8.22	10.98	8.81	9.00	9.08	9.31	11.27	10.10	8.55	12.55	11.06	8.17	9.55	7.84	10.16	10.25	9.15	9.50	9.93	10.79	11.52	10.26	9.78	11.65	11.12	8.52	8.54	8.40	10.72	7.04	10.59	9.00	9.14	8.95
SPEPEAAAAVPRRL	9.79	9.30	9.94	8.72	9.32	9.04	9.24	10.75	10.15	11.19	4.81	8.25	10.45	9.00	8.68	9.62	7.82	10.55	10.59	10.60	10.65	10.47	10.38	8.96	8.70	11.57	10.29	9.05	8.69	10.00	10.50	11.11	7.31	10.49	9.11	9.83	7.02	8.39	7.60	9.79	10.32	12.69	11.31	11.44	11.85
SVPRGEAAGAVQELARALAHLLEAERQE	11.00	6.53	7.67	10.16	9.39	9.87	9.69	9.92	9.12	11.22	9.18	7.15	8.77	8.23	9.69	7.10	9.72	11.78	10.54	9.35	10.48	7.43	10.36	8.72	8.93	8.61	9.40	10.29	9.35	9.92	10.29	9.55	7.39	10.13	11.75	10.60	9.22	9.02	9.70	10.82	10.16	11.30	9.07	9.64	10.06
VKMALQQEGFD	9.67	7.82	7.45	10.24	9.30	9.05	6.41	8.49	9.46	10.12	9.13	8.50	9.79	9.54	9.64	9.22	10.25	9.65	8.50	8.04	11.55	10.57	8.30	8.81	9.96	8.67	9.91	9.11	10.29	9.67	8.67	10.74	9.94	9.94	11.30	10.30	8.33	8.72	9.23	10.43	9.93	9.80	9.13	8.86	9.11
YGGFLRKYP	10.22	8.28	9.85	9.85	9.46	8.95	8.75	9.09	8.09	12.58	9.26	6.10	9.90	7.40	9.09	8.99	9.70	11.04	12.22	7.79	12.01	10.68	7.29	9.66	9.19	6.97	10.53	9.20	10.06	9.60	6.41	11.36	10.56	4.63	11.90	11.18	8.58	9.29	8.50	11.44	11.42	10.69	9.59	8.49	8.82
YGGFLRKYPK	11.39	8.40	9.99	10.23	8.73	8.21	9.69	8.38	9.67	9.94	9.20	5.26	9.66	8.54	10.11	8.22	10.51	10.92	9.84	7.76	10.77	10.52	9.47	9.26	8.00	9.97	7.52	8.98	9.61	9.02	9.92	10.92	7.28	9.53	11.42	10.79	9.34	8.74	10.20	11.34	8.25	10.30	8.87	7.99	9.10
GGFMRGL	9.15	7.73	9.25	11.09	9.40	6.71	9.33	7.52	8.27	5.81	7.89	9.03	10.76	9.44	9.08	9.05	5.67	9.33	8.68	8.25	13.07	10.82	10.00	9.37	9.91	9.33	11.05	9.86	9.72	10.04	6.24	8.49	9.17	11.25	10.77	8.30	8.86	8.37	9.98	9.44	11.87	6.88	10.53	9.53	9.41
LEDEAKELQ	11.92	9.56	9.56	11.04	7.53	5.07	10.83	9.00	8.89	4.48	8.78	9.28	9.81	7.93	9.77	8.19	10.69	8.17	8.21	7.25	9.01	9.69	9.02	8.67	8.83	9.77	9.25	9.04	10.00	9.22	10.69	8.12	7.45	8.67	9.31	9.75	9.69	8.36	10.28	10.22	9.36	7.06	9.67	8.49	5.48
MDELYPVEPEEEANGGEVL	10.49	8.39	9.73	11.13	7.74	8.90	5.82	7.94	10.00	12.03	7.18	10.55	11.18	9.75	10.75	8.93	10.09	12.16	10.69	9.79	11.34	11.03	10.62	10.43	4.86	3.56	10.37	10.79	10.88	11.24	10.57	11.79	10.92	10.31	12.26	11.97	8.53	9.76	8.21	10.78	12.00	13.47	10.46	9.50	9.32
MDELYPVEPEEEANGGEVLA	9.76	7.92	9.36	12.05	7.52	9.78	9.28	8.26	10.19	12.26	3.30	10.15	11.31	8.64	4.36	9.16	8.54	11.51	9.99	8.73	11.81	11.22	10.67	9.96	8.95	9.83	11.41	10.31	10.39	10.55	7.12	10.81	10.26	7.02	10.98	11.17	8.09	9.18	9.61	10.10	11.83	12.88	7.06	9.31	8.59
SPQLEDEAKEL	9.72	7.66	9.84	9.20	8.76	8.34	8.22	8.57	9.16	10.48	6.86	10.21	9.63	8.02	8.23	8.71	9.28	10.11	10.51	8.87	10.97	10.24	6.37	8.32	8.29	3.56	9.66	8.96	9.13	9.55	6.79	10.78	8.88	7.35	11.20	10.86	7.86	8.63	9.17	9.94	10.94	11.29	9.08	8.45	9.02
SPQLEDEAKELQ	10.54	7.78	8.11	8.45	7.62	8.69	9.48	7.34	7.74	11.38	6.49	6.02	9.95	6.24	10.17	7.85	6.88	10.21	9.64	6.90	11.38	7.28	7.53	9.41	9.59	5.33	10.68	9.46	8.26	9.18	5.74	10.72	10.72	10.23	10.85	11.41	9.06	2.10	9.90	10.69	8.14	11.24	9.03	7.95	9.42
VGRPEWWMDYQ	11.19	6.49	8.61	9.63	8.04	6.79	9.66	8.50	6.66	11.19	9.15	7.62	10.32	9.92	6.37	8.53	11.06	10.06	10.03	8.63	11.20	11.01	9.06	10.54	8.85	9.06	10.22	10.79	8.42	10.17	5.94	11.09	9.79	9.80	10.37	11.48	5.72	9.98	8.20	10.02	9.45	11.57	6.68	8.40	8.89
YGGFMRF	10.94	8.60	10.74	11.17	9.10	8.96	9.24	9.21	8.88	10.08	8.31	8.51	10.06	9.51	9.37	9.65	11.07	10.17	9.80	9.20	11.53	10.46	8.27	9.86	10.15	9.56	9.77	9.77	6.26	10.60	7.67	11.80	9.71	9.15	12.25	12.00	9.16	9.51	9.73	11.41	9.11	9.49	6.72	6.84	7.44
YGGFMRGL	9.98	7.67	7.15	11.00	8.49	9.27	8.59	8.16	6.26	10.67	8.94	9.18	9.45	9.54	8.70	8.59	9.80	9.74	9.55	8.35	11.11	8.63	8.75	9.23	9.69	9.30	10.81	9.24	10.45	10.35	9.22	11.23	9.12	8.06	11.47	11.11	7.53	9.68	8.91	9.54	10.01	10.52	8.11	7.21	9.59
A(+42.01)AYKLVLIRH	8.69	10.61	10.82	8.43	7.84	8.17	9.94	8.22	10.04	8.43	9.41	10.74	9.60	10.37	10.70	11.74	8.81	9.38	8.82	10.67	9.58	10.38	9.47	9.26	9.54	8.66	10.01	10.58	8.86	10.34	10.91	9.01	9.02	11.04	8.74	9.74	10.11	9.31	9.21	9.58	9.64	10.06	8.83	10.26	9.43
A(+42.01)AYKLVLIRHG	8.80	10.51	10.92	11.56	10.92	9.74	9.99	8.12	7.51	9.75	11.09	10.45	9.74	10.45	10.57	10.74	9.99	9.08	8.97	9.97	9.66	10.85	9.01	10.37	8.98	10.23	10.39	10.26	7.98	9.82	10.16	8.42	10.54	11.37	9.16	9.90	10.30	9.91	9.72	8.72	9.80	10.79	8.88	10.93	10.72
A(+42.01)AYKLVLIRHGE	9.37	9.87	10.23	10.88	9.98	9.15	9.49	7.48	9.48	8.76	11.16	9.80	9.68	9.71	10.72	10.64	9.80	8.13	8.66	9.56	8.92	10.35	9.24	9.85	9.99	9.96	10.24	9.83	11.07	8.98	10.67	9.04	9.57	10.46	6.80	9.43	10.52	9.80	10.05	8.84	9.82	9.26	8.06	9.99	10.41
TYNFAVLKLMG	8.68	10.68	11.03	9.58	11.01	9.26	9.88	11.79	8.11	8.55	8.56	12.09	11.67	9.40	9.56	9.76	10.06	5.60	8.29	11.21	11.76	11.85	10.37	9.24	10.75	12.96	10.06	9.74	9.61	8.10	10.62	6.95	7.51	10.08	4.05	7.91	7.94	9.88	10.34	7.48	9.86	9.86	9.21	10.77	10.25
TYNFAVLKLMGRG	6.35	6.02	9.62	8.64	8.15	7.55	8.38	12.32	4.04	6.37	9.30	10.39	5.76	8.08	7.49	10.64	8.43	4.60	6.71	7.28	10.49	8.32	8.52	6.05	9.47	12.63	6.39	9.52	9.69	2.54	8.03	5.83	3.04	9.08	1.51	6.96	6.38	8.50	9.26	5.21	8.06	1.65	7.21	4.15	11.05
TYNFAVLKLMGRGTKF	7.88	10.30	9.57	10.84	10.29	9.39	8.67	6.28	7.86	10.07	10.54	10.75	8.39	8.97	9.60	12.29	9.71	8.94	10.63	7.33	6.67	9.85	9.71	10.23	9.42	12.67	8.23	6.90	10.74	10.53	9.02	11.00	8.81	10.02	7.17	8.57	9.13	8.82	11.53	9.99	7.57	8.35	8.79	8.03	9.99
EIGDEENSAKFPI(-.98)	10.24	7.69	11.05	10.00	8.44	8.12	9.57	8.20	8.92	10.02	8.35	6.57	10.85	9.51	10.25	8.30	9.72	9.77	9.48	8.32	11.82	10.96	9.16	9.18	9.28	9.67	7.80	8.61	9.20	9.02	9.58	10.87	5.60	8.56	11.78	10.60	9.50	9.39	9.55	10.40	10.17	10.89	9.34	10.39	10.31
SFFAVMGA	11.98	5.82	9.71	8.64	8.53	8.39	8.91	11.55	7.36	7.85	6.48	7.24	9.99	9.85	9.12	8.91	9.34	10.87	7.58	11.12	10.79	9.25	8.62	3.57	9.88	7.91	9.19	9.99	9.36	7.60	9.42	6.09	7.80	9.65	4.14	8.00	8.82	8.42	8.07	8.11	8.71	11.25	10.18	12.39	11.83
MQIFVKTL	11.87	10.29	11.17	11.79	10.35	9.76	10.12	10.96	7.68	8.10	10.36	10.25	9.83	10.26	10.40	9.35	10.87	8.84	9.69	8.73	9.71	10.36	8.64	9.86	10.26	8.64	8.77	9.30	6.70	9.62	9.51	9.63	6.55	11.72	7.81	8.38	10.09	9.89	9.02	10.09	8.97	8.63	8.71	8.32	9.58
MQIFVKTLT	10.77	9.68	9.12	10.66	10.55	6.90	9.11	11.14	9.26	8.48	10.34	10.10	10.80	9.77	10.49	9.84	10.17	9.16	8.44	8.65	10.95	10.20	9.68	11.48	11.58	10.27	11.33	10.71	9.02	10.01	11.48	9.93	10.58	10.95	10.92	10.31	9.76	8.89	6.85	10.65	10.54	6.63	9.25	6.70	8.99
MQIFVKTLTGK	9.98	9.81	10.71	8.58	8.30	8.75	9.78	11.31	7.60	8.10	9.64	10.03	9.96	9.87	5.97	8.64	9.26	9.18	10.75	7.78	10.02	9.97	8.02	10.01	9.64	10.85	9.91	9.53	9.36	10.13	8.14	8.79	9.60	9.91	8.66	8.80	9.20	9.26	6.72	9.72	7.79	9.61	9.21	7.43	10.15
STLHLVLRLRGG	11.49	10.33	10.78	9.51	9.70	9.70	10.94	11.26	9.91	9.72	10.19	9.56	10.66	9.18	10.48	8.94	9.79	8.93	10.51	9.53	10.11	9.44	9.69	10.72	11.03	10.36	10.08	10.26	10.67	9.97	10.31	9.64	9.45	10.40	10.15	9.30	9.73	9.89	10.73	9.19	9.31	8.61	10.57	9.96	10.20
TLHLVLRLRGG	12.25	7.48	8.64	9.65	9.48	10.30	11.81	10.93	7.49	9.37	11.12	9.16	11.16	9.53	11.05	9.51	10.00	8.59	9.01	10.00	10.46	9.23	10.07	10.25	11.11	9.94	9.35	9.56	10.99	9.83	10.21	8.95	9.69	10.60	6.95	9.23	9.45	8.71	10.43	9.68	9.80	7.78	10.38	9.96	10.16
AFVLVLYDELKKVI	11.94	11.24	10.51	8.99	11.91	10.78	9.86	7.82	10.15	9.91	14.51	12.49	6.67	9.89	12.08	11.54	10.17	11.52	11.17	12.30	11.75	9.40	10.83	10.85	11.14	7.32	9.50	10.45	11.32	11.58	11.70	8.83	12.26	12.60	10.80	9.38	10.98	10.19	9.13	11.35	10.86	12.49	13.08	11.95	11.64
GAFVLVLYDELKKVI	12.68	11.03	10.52	11.33	10.81	11.12	9.62	9.49	10.80	10.61	8.73	10.11	11.90	9.36	9.10	10.95	9.28	11.92	10.57	11.68	11.66	11.00	10.16	10.93	10.73	12.60	9.44	10.20	11.05	11.63	11.92	10.92	12.74	12.96	11.30	9.90	9.48	10.32	10.83	11.45	11.83	12.06	12.60	9.74	8.47
M(+42.01)DVFMKGL	10.82	9.82	11.77	8.96	11.32	11.02	10.63	12.37	10.87	8.63	9.40	10.13	10.66	10.40	9.89	11.73	9.25	9.10	7.99	12.61	7.63	10.42	10.84	10.50	10.15	9.90	10.78	10.47	7.90	10.37	11.58	9.07	10.94	11.39	2.89	7.66	9.44	9.38	9.58	8.00	9.43	7.57	10.49	10.13	11.08
SHLGGAVF	9.73	7.86	10.73	7.15	11.99	7.86	10.56	5.66	8.72	6.34	8.20	9.95	9.69	10.37	9.54	9.11	9.13	7.12	4.35	8.75	7.75	9.36	8.74	6.86	9.04	9.98	9.30	10.88	11.56	10.16	9.29	7.72	8.90	7.87	3.88	4.90	9.61	7.45	9.45	5.41	8.68	9.74	7.83	8.69	10.04
APIGLKAVVG	9.35	9.64	10.96	10.85	10.38	9.33	10.63	7.97	9.77	8.56	10.74	9.66	10.31	8.84	9.73	9.98	10.19	9.41	8.29	8.76	9.39	11.46	9.19	9.86	9.46	10.19	9.73	10.29	10.52	9.29	10.89	10.18	10.11	11.37	11.01	11.01	11.00	10.12	9.09	10.65	10.27	10.50	8.98	9.22	10.11
ALNSVAYERNAMQNY	10.71	6.97	7.90	10.44	10.34	9.61	8.84	7.59	9.70	11.48	9.75	8.26	10.37	8.96	9.77	8.98	8.05	7.91	9.55	8.05	10.75	11.77	7.54	10.07	9.46	9.94	10.43	9.26	8.97	9.94	10.73	10.64	6.83	8.74	9.61	10.57	8.28	9.11	8.18	10.93	9.84	9.58	7.41	8.65	5.44
ALNSVAYERNAMQNYE	10.27	6.58	6.48	10.54	8.09	8.90	9.10	7.31	9.68	12.03	6.93	8.07	10.82	9.31	9.52	8.24	10.83	10.04	9.60	7.97	11.94	7.06	9.63	8.64	4.89	8.57	9.75	7.89	9.24	9.51	7.07	10.86	7.83	5.73	10.52	9.68	6.80	8.63	9.60	10.66	8.92	10.37	8.69	8.42	8.91
RPKPQQFFGLM(-.98)	10.54	7.09	8.09	10.52	9.44	8.14	8.72	9.17	8.96	9.90	9.90	9.36	10.30	9.47	9.83	10.09	10.99	9.60	9.43	8.77	11.78	9.41	8.52	9.81	10.51	10.83	9.75	9.57	9.29	10.21	10.25	10.18	8.57	10.76	10.75	9.98	8.93	9.16	10.13	10.03	9.35	8.10	7.53	7.87	8.72
S(+42.01)DKPDMAEIEKFDK	10.76	9.36	11.12	9.72	8.90	9.03	10.87	10.57	8.67	10.14	10.44	8.43	11.12	8.35	9.71	9.49	10.39	9.11	10.20	9.34	10.83	9.41	10.14	9.55	9.88	9.68	9.98	9.24	9.14	10.00	10.35	9.81	10.42	7.88	8.47	9.68	9.52	9.87	10.01	10.58	8.76	9.30	9.89	10.76	10.47
GASLKPEFVDIINAKQ	9.79	10.74	9.22	10.77	11.28	9.99	10.02	8.41	10.50	9.38	11.95	10.99	9.55	9.62	10.15	9.98	9.98	8.98	9.86	6.32	10.32	9.97	11.13	10.78	10.40	10.36	10.31	9.66	11.84	11.12	10.28	11.04	10.91	7.49	11.46	10.77	9.90	8.68	9.95	10.49	11.29	6.54	10.81	9.92	10.88
SLKPEFVDIINAKQ	9.87	10.02	10.36	9.01	10.41	10.05	10.25	9.12	9.63	9.35	10.44	7.61	10.65	9.48	9.74	9.96	9.45	9.27	9.13	10.56	9.19	7.75	9.94	9.69	9.97	11.06	10.47	9.05	9.13	9.90	10.53	9.89	9.20	9.14	8.04	9.39	9.64	9.31	10.01	9.05	10.21	9.59	9.40	9.28	11.31
ASWTREPLE	10.03	8.25	8.20	9.44	8.83	9.50	9.34	9.25	7.64	10.96	6.45	10.58	10.06	7.61	8.62	8.89	8.62	11.55	9.82	8.16	11.02	9.42	9.27	9.07	7.66	5.78	10.71	9.10	9.27	9.43	9.88	11.76	9.52	8.88	12.57	11.22	8.49	8.27	9.21	11.23	9.95	11.14	7.84	8.18	7.31
ASWTREPLEE	5.12	8.98	9.46	7.65	8.88	7.65	11.95	8.86	9.36	9.79	10.22	10.03	9.89	7.32	8.75	8.94	9.82	10.21	9.69	7.96	11.05	8.06	7.59	9.52	6.92	10.56	10.89	9.92	8.27	9.30	6.71	10.73	7.19	9.71	11.05	11.82	8.27	9.81	9.89	11.50	10.32	10.10	7.92	8.07	8.55
EDEAAWSLDRTQQ	10.28	7.88	9.23	7.80	8.42	7.48	8.29	8.31	8.44	10.46	9.07	9.61	10.50	8.65	9.73	7.52	9.57	11.05	9.90	8.34	11.95	7.69	8.48	9.34	8.57	5.26	10.06	8.92	9.04	9.27	10.15	11.18	9.96	6.69	12.22	11.71	8.58	8.12	8.72	11.76	8.53	10.67	8.38	8.52	7.50
FLVFHSFGGG	9.26	7.79	9.17	9.77	9.99	8.03	6.42	11.73	6.41	10.25	11.85	10.43	5.85	9.37	9.55	11.39	10.98	6.59	11.61	6.84	10.82	11.22	6.99	10.34	7.12	11.31	11.37	8.90	10.93	10.01	11.13	9.45	5.55	8.40	7.02	6.91	6.50	10.14	9.09	8.75	9.21	8.59	10.18	8.19	9.72
GLQGFLVFH	10.30	10.81	10.94	5.54	10.64	9.35	8.99	8.03	8.71	7.51	7.38	11.40	9.80	9.13	9.53	10.44	8.43	6.77	6.99	11.72	10.00	9.11	8.37	7.61	8.87	10.02	7.68	6.82	10.17	8.60	9.39	7.61	8.50	9.58	10.38	6.43	8.94	9.04	9.15	5.28	8.59	5.04	8.53	8.02	10.13
LQGFLVFH	8.08	7.14	10.11	10.19	9.35	7.96	8.38	7.93	8.58	6.59	7.68	9.46	6.45	7.34	9.04	10.39	7.03	3.63	6.42	7.20	3.95	7.18	8.09	6.98	7.98	9.56	7.92	8.32	10.13	5.37	9.58	7.87	8.71	8.22	3.73	7.74	8.61	8.36	8.29	7.38	9.17	6.21	7.68	7.42	9.79
SGFTSLLMERL	10.48	8.38	10.11	10.53	6.20	7.42	8.93	5.66	10.26	7.68	6.94	10.71	4.49	8.75	10.31	9.90	8.76	8.69	8.74	12.43	10.80	8.57	9.30	9.57	9.96	11.49	7.91	9.55	10.75	9.16	9.61	6.70	9.01	11.61	12.72	8.12	9.32	9.21	9.82	8.99	8.71	9.26	10.52	11.58	11.25
SIYPAPQVS	8.07	8.81	10.42	8.22	10.20	8.33	9.45	6.90	6.02	5.96	10.18	9.11	9.07	8.36	8.01	9.10	6.95	11.57	5.14	4.75	10.70	8.89	8.59	8.00	8.72	10.25	7.65	7.34	11.32	9.33	9.55	7.92	8.84	8.74	4.13	7.71	9.42	9.23	9.41	7.80	8.69	5.19	6.72	6.38	7.44
TGLQGFLVFH	6.80	6.24	8.83	6.45	11.11	7.17	7.47	6.41	7.84	5.96	7.70	8.51	6.42	7.13	8.05	7.46	6.07	3.73	4.22	2.90	0.32	8.14	7.84	4.45	8.33	8.76	6.65	8.71	10.37	8.98	8.40	7.31	7.36	7.10	10.48	5.13	8.10	7.68	8.55	6.55	6.70	2.33	6.43	6.19	8.93
TGLQGFLVFHSFGGG	6.33	10.76	8.60	9.41	9.19	8.36	8.61	12.43	10.09	9.68	9.56	9.99	11.31	9.00	7.97	5.79	9.44	6.74	8.67	8.36	10.51	7.37	9.71	9.51	9.17	10.92	8.98	10.06	9.12	8.42	10.16	7.63	9.96	10.55	12.07	8.13	8.69	11.38	11.56	7.67	10.15	11.41	10.67	11.45	9.87
TSLLMERL	7.85	6.72	10.80	9.13	8.56	6.99	9.02	6.38	8.50	5.66	7.55	10.12	7.65	8.27	4.45	10.50	6.52	5.47	6.40	7.48	4.64	9.02	8.00	7.96	8.10	9.93	6.92	10.12	4.78	7.06	9.23	1.31	8.44	8.73	6.16	7.84	9.75	7.12	6.97	4.88	6.67	6.68	4.32	6.69	5.49
SGPFGQIFRPDNFVFGQ	8.83	5.91	9.97	9.41	10.08	10.30	9.91	12.58	10.29	8.27	7.91	12.29	11.34	9.94	7.13	8.10	9.10	7.31	8.75	8.53	11.76	11.14	10.79	10.76	10.04	7.55	9.90	10.89	8.36	9.33	9.39	9.20	9.35	9.96	11.61	7.82	8.39	10.12	10.41	7.21	8.55	9.80	10.53	10.40	10.81

Peak intensity plots

EigenMS removes sample-to-sample variability.

Intensity after log2 transformation

Intensity after EigenMS normalization

Univariate analysis

Univariate statistic analysis will proceed for each pairs of comparison. For each pair,

Step 1, differential analysis;

• t-test

• Wilcoxon rank-sum test

For all statistical tests, the Benjamini-Hochberg (BH) procedure was applied to correct for multiple hypothesis testing.

Step 2, fold change, both linear and log2;

Step 3, regulation shown in volcano plot.

• A feature is considered unregulated when FC(log2) > 0.6 (or FC(lin) > 1.5);

• A feature is considered downregulated when FC(log2) < -0.6 (or FC(lin) < -1.5).

Code

d5 <- rbind.data.frame(labels_d1, norm_d1_mod) 
d5_mod <- t(d5) %>%
  as.data.frame(.) %>%
  rownames_to_column(., var = "rowname") %>%
  as_tibble() %>%
  dplyr::rename(., Label = class) %>%
  mutate(across(-c(Label,rowname), as.numeric)) %>%
  #rename_with(str_trim)
  column_to_rownames(., var = "rowname")

#colnames(d5_mod)[-1] == feature_name$variable
colnames(d5_mod)[-1] = feature_name$name

grps = as.factor(t(labels_d1))
trt= levels(grps)

combo_list = do.call("c", lapply(seq_along(time), function(i) combn(trt, 2, FUN = list))) # top 10 are unique combo
#combo_list = combo_list[1:10]

feature_meta = read.csv(file = "feature_meta_hypo.csv")

folder = paste(getwd(), "/hypo/", sep = "")

August vs IBA

Full stat

Code

contrast = combo_list[[1]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: August over IBA"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
A(+42.01)AYKLVLIRH	0.351	0.689	0.277	0.563	0.737	-0.441	0.563	0.249	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHG	0.505	0.782	0.815	0.931	1.155	0.208	0.782	0.107	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHGE	0.243	0.567	0.370	0.669	1.271	0.346	0.567	0.247	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)GQAFRKFLPLFDRVLVER	0.822	0.945	1.000	1.000	1.280	0.356	0.945	0.025	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
A(+42.01)LLRGVFIVAAKR	0.833	0.945	1.000	1.000	1.155	0.208	0.945	0.025	tr|I3N5Y9|I3N5Y9_ICTTR	Acetyl-CoA acyltransferase 2	ACAA2
AADQDLGPEAPPEGVLGA	0.700	0.881	0.888	0.948	1.567	0.648	0.881	0.055	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.094	0.350	0.167	0.520	2.641	1.401	0.350	0.456	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALL	0.857	0.950	0.963	0.998	0.929	-0.106	0.950	0.022	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALLRV	0.962	0.978	0.888	0.948	1.015	0.021	0.948	0.023	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AEALERMFL	0.664	0.872	0.815	0.931	1.095	0.131	0.872	0.059	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
AFQKVVAGVANALSHKYH	0.840	0.945	0.815	0.931	0.890	-0.169	0.931	0.031	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
AFVLVLYDELKKVI	0.128	0.424	0.236	0.550	0.505	-0.986	0.424	0.373	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
ALNSVAYERNAMQNY	0.057	0.306	0.021	0.165	1.476	0.562	0.165	0.782	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
ALNSVAYERNAMQNYE	0.003	0.091	0.006	0.123	2.684	1.424	0.091	1.042	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
APIGLKAVVG	0.384	0.722	0.200	0.550	1.095	0.131	0.550	0.259	tr|A0A287D563|A0A287D563_ICTTR	Syntaxin binding protein 1	STXBP1
ASWTREPLE	0.017	0.166	0.036	0.192	1.849	0.887	0.166	0.780	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
ASWTREPLEE	0.253	0.578	0.167	0.520	2.334	1.223	0.520	0.284	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
DIDTAAKFIGAGAA	0.876	0.962	0.541	0.809	1.015	0.021	0.809	0.092	tr|I3MKX8|I3MKX8_ICTTR	ATP synthase lipid-binding protein	ATP5MC1
DILGKYVD	0.544	0.801	0.200	0.550	2.191	1.132	0.550	0.259	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
EDEAAWSLDRTQQ	0.032	0.202	0.021	0.165	1.996	0.997	0.165	0.782	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
EIGDEENSAKFPI(-.98)	0.210	0.544	0.277	0.563	1.370	0.455	0.544	0.265	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
FLGEAYHHVPESQ	0.018	0.166	0.021	0.165	2.764	1.467	0.165	0.782	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.002	0.086	0.004	0.104	3.086	1.626	0.086	1.067	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLVFHSFGGG	0.088	0.350	0.093	0.358	2.073	1.052	0.350	0.456	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
GAAAQSLYIANHAY	0.953	0.978	1.000	1.000	1.119	0.162	0.978	0.010	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
GAEALERMFL	0.042	0.248	0.036	0.192	0.645	-0.632	0.192	0.717	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
GAFVLVLYDELKKVI	0.981	0.981	0.888	0.948	1.015	0.022	0.948	0.023	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
GASLKPEFVDIINAKQ	0.336	0.684	0.673	0.919	1.209	0.273	0.684	0.165	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
GGFMRGL	0.444	0.750	0.236	0.550	1.877	0.909	0.550	0.259	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GLQGFLVFH	0.495	0.782	0.673	0.919	0.651	-0.620	0.782	0.107	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
KVVAGVANALSHKYH	0.462	0.760	0.673	0.919	1.254	0.326	0.760	0.119	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
LEDEAKELQ	0.016	0.166	0.015	0.165	3.132	1.647	0.165	0.782	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
LENPQPQAPA	0.032	0.202	0.021	0.165	2.883	1.528	0.165	0.782	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LENPQPQAPARRLLPP	0.140	0.437	0.236	0.550	1.753	0.810	0.437	0.359	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGVLFNPYYDPLQWKSSRFE	0.005	0.109	0.011	0.155	1.833	0.874	0.109	0.963	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LQGFLVFH	0.670	0.872	0.423	0.678	1.288	0.365	0.678	0.169	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
M(+42.01)DVFMKGL	0.049	0.272	0.074	0.347	0.567	-0.819	0.272	0.566	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
MDELYPVEPEEEANGGEVL	0.070	0.339	0.114	0.412	1.543	0.625	0.339	0.470	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MDELYPVEPEEEANGGEVLA	0.129	0.424	0.167	0.520	1.944	0.959	0.424	0.373	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MQIFVKTL	0.016	0.166	0.011	0.155	3.063	1.615	0.155	0.808	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLT	0.011	0.166	0.008	0.147	2.273	1.185	0.147	0.831	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLTGK	0.090	0.350	0.059	0.288	1.625	0.700	0.288	0.540	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
PMFVVNTNVPRA	0.967	0.978	0.815	0.931	0.987	-0.019	0.931	0.031	tr|I3N9F5|I3N9F5_ICTTR	Macrophage migration inhibitory factor	MIF
PVNFKLL	0.651	0.872	0.963	0.998	0.520	-0.944	0.872	0.059	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
PYQYPAL	0.958	0.978	0.888	0.948	0.901	-0.150	0.948	0.023	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
Q(-17.03)EDAELQP	0.018	0.166	0.027	0.192	1.988	0.992	0.166	0.780	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)EDAELQPR	0.171	0.484	0.321	0.600	1.606	0.683	0.484	0.316	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)YDRVAELDQLLHY	0.081	0.350	0.059	0.288	1.389	0.474	0.288	0.540	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPKPQQFFGLM(-.98)	0.000	0.008	0.000	0.018	2.894	1.533	0.008	2.099	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
RTLYGFGG	0.173	0.484	0.236	0.550	1.296	0.374	0.484	0.316	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
S(+42.01)DKPDMAEIEKFDK	0.293	0.643	0.321	0.600	1.307	0.387	0.600	0.222	tr|A0A287CVS2|A0A287CVS2_ICTTR	Thymosin beta	Tmsb4x
S(+42.01)ILKIHAREIFD	0.610	0.839	0.481	0.758	1.237	0.307	0.758	0.120	tr|I3MIE7|I3MIE7_ICTTR	2-phospho-D-glycerate hydro-lyase	ENO1
SAMLIQKL	0.132	0.424	0.167	0.520	1.365	0.449	0.424	0.373	tr|I3M435|I3M435_ICTTR	Acetyl-CoA acetyltransferase 1	ACAT1
SAVISLEGKPL	0.614	0.839	0.888	0.948	1.123	0.168	0.839	0.076	tr|I3MY03|I3MY03_ICTTR	Cofilin, non-muscle isoform	CFL1
SESLFVSNHAY	0.431	0.743	0.423	0.678	1.118	0.162	0.678	0.169	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SFFAVMGA	0.428	0.743	0.743	0.931	0.715	-0.484	0.743	0.129	tr|A0A287CVH5|A0A287CVH5_ICTTR	Polypyrimidine tract binding protein 2	PTBP2
SGFAAPFFIVRHQLLKK	0.969	0.978	0.815	0.931	0.753	-0.409	0.931	0.031	tr|A0A287CU43|A0A287CU43_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967835
SGFTSLLMERL	0.200	0.534	0.370	0.669	0.440	-1.185	0.534	0.273	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SGPFGQIFRPDNFVFGQ	0.196	0.534	0.236	0.550	0.732	-0.449	0.534	0.273	tr|I3NEP5|I3NEP5_ICTTR	Tubulin beta chain	TUBB2B
SGSAKVAFSAIRSTNH	0.097	0.350	0.093	0.358	1.661	0.732	0.350	0.456	tr|I3MWG7|I3MWG7_ICTTR	GST class-pi	GSTP1
SHLGGAVF	0.966	0.978	0.743	0.931	1.017	0.024	0.931	0.031	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
SIGRFFG	0.391	0.722	0.541	0.809	1.069	0.096	0.722	0.141	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGG	0.393	0.722	0.743	0.931	1.134	0.181	0.722	0.141	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGGDRG	0.770	0.917	0.815	0.931	1.446	0.532	0.917	0.037	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIYPAPQVS	0.119	0.418	0.236	0.550	1.483	0.569	0.418	0.379	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SLDKFLA	0.753	0.907	0.743	0.931	1.517	0.601	0.907	0.042	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLDKFLASVSTVLTSKYR	0.404	0.731	0.423	0.678	0.934	-0.099	0.678	0.169	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLFVSNHAY	0.695	0.881	0.815	0.931	1.056	0.078	0.881	0.055	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SLKPEFVDIINAKQ	0.165	0.484	0.236	0.550	1.311	0.391	0.484	0.316	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
SLSAASPPMTEAGTPRRF	0.538	0.801	0.321	0.600	1.238	0.308	0.600	0.222	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SLYIANHAY	0.527	0.798	0.815	0.931	1.058	0.082	0.798	0.098	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
SPEPEAAAAVPRRL	0.449	0.750	0.200	0.550	0.657	-0.606	0.550	0.259	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SPQLEDEAKEL	0.073	0.340	0.036	0.192	1.663	0.734	0.192	0.717	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.218	0.544	0.277	0.563	1.621	0.697	0.544	0.265	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SSPETLISDLLMRESTENVPRTRLEDPSMW	0.431	0.743	0.277	0.563	1.961	0.972	0.563	0.249	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY
STLHLVLRLRGG	0.238	0.566	0.277	0.563	1.394	0.479	0.563	0.249	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
SVLISLKQAPLVH	0.587	0.834	0.606	0.870	1.071	0.099	0.834	0.079	tr|A0A287D1C0|A0A287D1C0_ICTTR	Clathrin light chain	CLTA
SVPRGEAAGAVQELARALAHLLEAERQE	0.236	0.566	0.423	0.678	1.353	0.436	0.566	0.247	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SVSTVLTSKYR	0.844	0.945	0.673	0.919	0.997	-0.005	0.919	0.037	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TAYAIYELAKA	0.740	0.907	0.423	0.678	1.147	0.197	0.678	0.169	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TAYAIYELAKASFPKKQD	0.835	0.945	0.888	0.948	1.096	0.132	0.945	0.025	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TDYLMKIL	0.661	0.872	0.423	0.678	0.307	-1.702	0.678	0.169	tr|I3MNL1|I3MNL1_ICTTR	Actin beta	ACTB
TGLQGFLVFH	0.596	0.834	0.321	0.600	0.745	-0.424	0.600	0.222	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TGLQGFLVFHSFGGG	0.592	0.834	0.606	0.870	0.817	-0.291	0.834	0.079	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
THYKLVPHQFAH	0.307	0.649	0.423	0.678	1.149	0.200	0.649	0.188	tr|I3MGG0|I3MGG0_ICTTR	Cytochrome c oxidase polypeptide Vb	LOC101965209
TIDFPEFL	0.495	0.782	0.093	0.358	0.610	-0.712	0.358	0.446	tr|I3MRD3|I3MRD3_ICTTR	Calmodulin	CALM1
TLHLVLRLRGG	0.166	0.484	0.541	0.809	1.768	0.822	0.484	0.316	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
TLSKIFKLGGKDSRSGSPMARR	0.092	0.350	0.093	0.358	1.802	0.849	0.350	0.456	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
TLYGFGG	0.332	0.684	0.541	0.809	1.262	0.336	0.684	0.165	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TPAVHASLDKFLA	0.349	0.689	0.200	0.550	1.266	0.340	0.550	0.259	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPAVHASLDKFLASVSTVLTSKYR	0.500	0.782	0.277	0.563	1.226	0.294	0.563	0.249	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPEAQAAFQKVVAGVANALSHKYH	0.736	0.907	0.888	0.948	0.868	-0.203	0.907	0.042	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
TSLLMERL	0.689	0.881	0.423	0.678	0.628	-0.672	0.678	0.169	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TTMIIDHVVPEPG	0.570	0.830	0.139	0.486	1.423	0.509	0.486	0.314	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TVVYGEPITA	0.510	0.782	0.321	0.600	1.663	0.734	0.600	0.222	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TYFPHFDL	0.393	0.722	0.815	0.931	1.102	0.140	0.722	0.141	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYFPHFDLSHG	0.749	0.907	0.963	0.998	1.295	0.373	0.907	0.042	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYNFAVLKLMG	0.836	0.945	0.815	0.931	0.809	-0.306	0.931	0.031	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRG	0.926	0.978	0.815	0.931	0.750	-0.415	0.931	0.031	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRGTKF	0.278	0.622	0.277	0.563	1.759	0.815	0.563	0.249	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
VGRPEWWMDYQ	0.019	0.166	0.036	0.192	1.975	0.982	0.166	0.780	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.061	0.310	0.114	0.412	1.400	0.485	0.310	0.509	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGFG	0.089	0.350	0.093	0.358	0.665	-0.588	0.350	0.456	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGR	0.894	0.972	1.000	1.000	1.038	0.054	0.972	0.012	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGRIG	0.306	0.649	0.606	0.870	0.872	-0.198	0.649	0.188	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VPPVQVSPLIKL	0.028	0.193	0.021	0.165	2.037	1.026	0.165	0.782	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
VPPVQVSPLIKLGRY	0.935	0.978	0.743	0.931	1.185	0.245	0.931	0.031	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
YGGFLRKYP	0.025	0.193	0.036	0.192	1.810	0.856	0.192	0.717	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFLRKYPK	0.214	0.544	0.236	0.550	1.789	0.839	0.544	0.265	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFMRF	0.008	0.148	0.004	0.104	2.462	1.300	0.104	0.984	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.001	0.040	0.000	0.018	3.081	1.624	0.018	1.735	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY(-.98)	0.026	0.193	0.036	0.192	1.821	0.865	0.192	0.717	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	status	Accession	Name	GN
RPKPQQFFGLM(-.98)	0.000	0.008	0	0.018	2.894	1.533	0.008	2.099	Up	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
YGGFMRGL	0.001	0.040	0	0.018	3.081	1.624	0.018	1.735	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

August vs March

Full stat

Code

contrast = combo_list[[2]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: August over March"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
A(+42.01)AYKLVLIRH	0.455	0.614	0.236	0.383	1.580	0.660	0.383	0.417	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHG	0.037	0.123	0.074	0.170	1.611	0.688	0.123	0.909	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHGE	0.007	0.042	0.006	0.034	1.641	0.715	0.034	1.465	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)GQAFRKFLPLFDRVLVER	0.063	0.169	0.139	0.259	1.616	0.693	0.169	0.773	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
A(+42.01)LLRGVFIVAAKR	0.001	0.020	0.001	0.012	2.526	1.337	0.012	1.911	tr|I3N5Y9|I3N5Y9_ICTTR	Acetyl-CoA acyltransferase 2	ACAA2
AADQDLGPEAPPEGVLGA	0.159	0.279	0.167	0.297	0.635	-0.655	0.279	0.555	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.106	0.202	0.236	0.383	1.457	0.543	0.202	0.695	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALL	0.003	0.026	0.000	0.009	0.230	-2.118	0.009	2.036	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALLRV	0.076	0.174	0.027	0.102	0.433	-1.207	0.102	0.990	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AEALERMFL	0.012	0.058	0.021	0.083	2.529	1.339	0.058	1.237	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
AFQKVVAGVANALSHKYH	0.019	0.079	0.011	0.054	2.322	1.215	0.054	1.267	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
AFVLVLYDELKKVI	0.965	0.966	0.815	0.877	1.030	0.043	0.877	0.057	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
ALNSVAYERNAMQNY	0.966	0.966	0.673	0.793	0.900	-0.152	0.793	0.101	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
ALNSVAYERNAMQNYE	0.120	0.220	0.321	0.480	0.603	-0.730	0.220	0.658	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
APIGLKAVVG	0.044	0.138	0.046	0.121	1.529	0.613	0.121	0.918	tr|A0A287D563|A0A287D563_ICTTR	Syntaxin binding protein 1	STXBP1
ASWTREPLE	0.747	0.858	0.888	0.921	1.141	0.190	0.858	0.066	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
ASWTREPLEE	0.095	0.187	0.074	0.170	1.952	0.965	0.170	0.769	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
DIDTAAKFIGAGAA	0.366	0.554	0.370	0.539	1.901	0.927	0.539	0.269	tr|I3MKX8|I3MKX8_ICTTR	ATP synthase lipid-binding protein	ATP5MC1
DILGKYVD	0.051	0.150	0.046	0.121	1.764	0.819	0.121	0.918	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
EDEAAWSLDRTQQ	0.517	0.681	0.673	0.793	1.054	0.077	0.681	0.167	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
EIGDEENSAKFPI(-.98)	0.744	0.858	0.815	0.877	1.130	0.177	0.858	0.066	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
FLGEAYHHVPESQ	0.406	0.598	0.541	0.697	1.294	0.372	0.598	0.223	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.364	0.554	0.606	0.746	0.792	-0.336	0.554	0.256	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLVFHSFGGG	0.010	0.054	0.015	0.066	2.638	1.400	0.054	1.265	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
GAAAQSLYIANHAY	0.089	0.181	0.139	0.259	3.193	1.675	0.181	0.743	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
GAEALERMFL	0.041	0.132	0.015	0.066	2.038	1.027	0.066	1.183	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
GAFVLVLYDELKKVI	0.910	0.935	1.000	1.000	1.091	0.126	0.935	0.029	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
GASLKPEFVDIINAKQ	0.825	0.900	0.743	0.841	1.070	0.097	0.841	0.075	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
GGFMRGL	0.860	0.900	0.673	0.793	0.956	-0.065	0.793	0.101	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GLQGFLVFH	0.010	0.054	0.006	0.034	1.969	0.977	0.034	1.465	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
KVVAGVANALSHKYH	0.851	0.900	0.481	0.657	2.046	1.033	0.657	0.183	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
LEDEAKELQ	0.641	0.798	0.541	0.697	1.398	0.484	0.697	0.157	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
LENPQPQAPA	0.714	0.844	0.541	0.697	0.967	-0.049	0.697	0.157	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LENPQPQAPARRLLPP	0.289	0.462	0.481	0.657	1.401	0.486	0.462	0.336	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGVLFNPYYDPLQWKSSRFE	0.034	0.115	0.046	0.121	0.566	-0.822	0.115	0.938	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LQGFLVFH	0.000	0.007	0.001	0.011	3.172	1.665	0.007	2.131	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
M(+42.01)DVFMKGL	0.491	0.655	0.277	0.424	1.130	0.177	0.424	0.372	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
MDELYPVEPEEEANGGEVL	0.146	0.259	0.093	0.196	0.614	-0.703	0.196	0.708	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MDELYPVEPEEEANGGEVLA	0.079	0.177	0.059	0.144	0.474	-1.077	0.144	0.841	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MQIFVKTL	0.016	0.073	0.027	0.102	2.585	1.370	0.073	1.137	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLT	0.088	0.181	0.200	0.339	1.698	0.764	0.181	0.743	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLTGK	0.081	0.179	0.059	0.144	1.963	0.973	0.144	0.841	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
PMFVVNTNVPRA	0.052	0.150	0.059	0.144	1.858	0.894	0.144	0.841	tr|I3N9F5|I3N9F5_ICTTR	Macrophage migration inhibitory factor	MIF
PVNFKLL	0.058	0.161	0.046	0.121	1.644	0.717	0.121	0.918	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
PYQYPAL	0.003	0.026	0.000	0.009	2.936	1.554	0.009	2.036	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
Q(-17.03)EDAELQP	0.001	0.020	0.002	0.015	0.407	-1.298	0.015	1.836	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)EDAELQPR	0.859	0.900	0.888	0.921	0.979	-0.031	0.900	0.046	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)YDRVAELDQLLHY	0.029	0.108	0.036	0.115	0.571	-0.807	0.108	0.965	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPKPQQFFGLM(-.98)	0.020	0.079	0.036	0.115	2.326	1.218	0.079	1.105	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
RTLYGFGG	0.007	0.042	0.011	0.054	1.956	0.968	0.042	1.374	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
S(+42.01)DKPDMAEIEKFDK	0.802	0.898	0.963	0.980	1.056	0.078	0.898	0.047	tr|A0A287CVS2|A0A287CVS2_ICTTR	Thymosin beta	Tmsb4x
S(+42.01)ILKIHAREIFD	0.005	0.031	0.004	0.026	2.529	1.339	0.026	1.586	tr|I3MIE7|I3MIE7_ICTTR	2-phospho-D-glycerate hydro-lyase	ENO1
SAMLIQKL	0.186	0.316	0.114	0.224	1.901	0.927	0.224	0.650	tr|I3M435|I3M435_ICTTR	Acetyl-CoA acetyltransferase 1	ACAT1
SAVISLEGKPL	0.085	0.181	0.008	0.044	1.728	0.789	0.044	1.354	tr|I3MY03|I3MY03_ICTTR	Cofilin, non-muscle isoform	CFL1
SESLFVSNHAY	0.020	0.079	0.036	0.115	1.522	0.606	0.079	1.105	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SFFAVMGA	0.681	0.837	0.743	0.841	0.703	-0.508	0.837	0.077	tr|A0A287CVH5|A0A287CVH5_ICTTR	Polypyrimidine tract binding protein 2	PTBP2
SGFAAPFFIVRHQLLKK	0.069	0.172	0.074	0.170	2.212	1.145	0.170	0.769	tr|A0A287CU43|A0A287CU43_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967835
SGFTSLLMERL	0.751	0.858	0.481	0.657	1.067	0.094	0.657	0.183	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SGPFGQIFRPDNFVFGQ	0.438	0.600	0.277	0.424	1.009	0.013	0.424	0.372	tr|I3NEP5|I3NEP5_ICTTR	Tubulin beta chain	TUBB2B
SGSAKVAFSAIRSTNH	0.858	0.900	1.000	1.000	1.025	0.036	0.900	0.046	tr|I3MWG7|I3MWG7_ICTTR	GST class-pi	GSTP1
SHLGGAVF	0.075	0.174	0.046	0.121	2.225	1.154	0.121	0.918	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
SIGRFFG	0.002	0.026	0.001	0.012	4.276	2.096	0.012	1.911	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGG	0.004	0.028	0.015	0.066	4.614	2.206	0.028	1.560	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGGDRG	0.095	0.187	0.093	0.196	1.615	0.691	0.187	0.728	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIYPAPQVS	0.004	0.029	0.002	0.020	3.369	1.753	0.020	1.705	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SLDKFLA	0.000	0.012	0.001	0.011	2.929	1.550	0.011	1.969	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLDKFLASVSTVLTSKYR	0.946	0.963	0.888	0.921	1.152	0.205	0.921	0.036	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLFVSNHAY	0.001	0.015	0.001	0.012	1.976	0.982	0.012	1.911	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SLKPEFVDIINAKQ	0.235	0.387	0.167	0.297	1.706	0.770	0.297	0.527	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
SLSAASPPMTEAGTPRRF	0.782	0.884	0.815	0.877	1.000	0.000	0.877	0.057	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SLYIANHAY	0.052	0.150	0.046	0.121	1.676	0.745	0.121	0.918	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
SPEPEAAAAVPRRL	0.716	0.844	0.743	0.841	1.162	0.217	0.841	0.075	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SPQLEDEAKEL	0.434	0.600	0.606	0.746	0.935	-0.097	0.600	0.222	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.288	0.462	0.423	0.600	0.729	-0.456	0.462	0.336	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SSPETLISDLLMRESTENVPRTRLEDPSMW	0.179	0.309	0.370	0.539	1.281	0.357	0.309	0.511	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY
STLHLVLRLRGG	0.439	0.600	0.277	0.424	1.184	0.244	0.424	0.372	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
SVLISLKQAPLVH	0.065	0.171	0.093	0.196	1.587	0.666	0.171	0.768	tr|A0A287D1C0|A0A287D1C0_ICTTR	Clathrin light chain	CLTA
SVPRGEAAGAVQELARALAHLLEAERQE	0.551	0.709	0.606	0.746	0.878	-0.188	0.709	0.149	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SVSTVLTSKYR	0.353	0.549	0.114	0.224	2.993	1.581	0.224	0.650	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TAYAIYELAKA	0.029	0.108	0.036	0.115	2.149	1.103	0.108	0.965	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TAYAIYELAKASFPKKQD	0.232	0.387	0.046	0.121	1.551	0.634	0.121	0.918	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TDYLMKIL	0.133	0.240	0.200	0.339	1.120	0.164	0.240	0.620	tr|I3MNL1|I3MNL1_ICTTR	Actin beta	ACTB
TGLQGFLVFH	0.033	0.114	0.021	0.083	3.172	1.666	0.083	1.083	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TGLQGFLVFHSFGGG	0.811	0.899	0.963	0.980	0.921	-0.119	0.899	0.046	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
THYKLVPHQFAH	0.526	0.685	0.815	0.877	1.323	0.403	0.685	0.164	tr|I3MGG0|I3MGG0_ICTTR	Cytochrome c oxidase polypeptide Vb	LOC101965209
TIDFPEFL	0.433	0.600	0.541	0.697	1.525	0.609	0.600	0.222	tr|I3MRD3|I3MRD3_ICTTR	Calmodulin	CALM1
TLHLVLRLRGG	0.829	0.900	0.815	0.877	1.017	0.024	0.877	0.057	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
TLSKIFKLGGKDSRSGSPMARR	0.011	0.056	0.011	0.054	2.596	1.376	0.054	1.267	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
TLYGFGG	0.089	0.181	0.167	0.297	1.649	0.721	0.181	0.743	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TPAVHASLDKFLA	0.076	0.174	0.139	0.259	2.042	1.030	0.174	0.760	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPAVHASLDKFLASVSTVLTSKYR	0.611	0.778	0.606	0.746	1.980	0.986	0.746	0.127	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPEAQAAFQKVVAGVANALSHKYH	0.074	0.174	0.114	0.224	1.790	0.840	0.174	0.760	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
TSLLMERL	0.097	0.188	0.046	0.121	2.512	1.329	0.121	0.918	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TTMIIDHVVPEPG	0.030	0.108	0.036	0.115	3.182	1.670	0.108	0.965	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TVVYGEPITA	0.000	0.010	0.000	0.009	5.379	2.427	0.009	2.036	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TYFPHFDL	0.003	0.026	0.002	0.015	2.330	1.220	0.015	1.836	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYFPHFDLSHG	0.000	0.009	0.000	0.009	4.017	2.006	0.009	2.053	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYNFAVLKLMG	0.069	0.172	0.114	0.224	2.050	1.035	0.172	0.765	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRG	0.003	0.026	0.004	0.026	7.646	2.935	0.026	1.586	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRGTKF	0.003	0.026	0.002	0.015	4.900	2.293	0.015	1.836	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
VGRPEWWMDYQ	0.637	0.798	0.743	0.841	0.567	-0.820	0.798	0.098	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.418	0.599	0.673	0.793	0.785	-0.349	0.599	0.222	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGFG	0.385	0.575	0.236	0.383	2.011	1.008	0.383	0.417	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGR	0.301	0.476	0.321	0.480	1.155	0.208	0.476	0.323	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGRIG	0.688	0.837	0.277	0.424	1.457	0.543	0.424	0.372	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VPPVQVSPLIKL	0.001	0.015	0.002	0.020	2.357	1.237	0.015	1.817	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
VPPVQVSPLIKLGRY	0.012	0.058	0.008	0.044	2.592	1.374	0.044	1.354	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
YGGFLRKYP	0.117	0.219	0.200	0.339	0.540	-0.889	0.219	0.660	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFLRKYPK	0.895	0.928	0.423	0.600	1.159	0.213	0.600	0.222	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFMRF	0.704	0.844	0.888	0.921	1.108	0.149	0.844	0.074	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.412	0.599	0.541	0.697	1.225	0.292	0.599	0.222	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY(-.98)	0.063	0.169	0.093	0.196	1.700	0.766	0.169	0.773	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	status	Accession	Name	GN
A(+42.01)AYKLVLIRHGE	0.007	0.042	0.006	0.034	1.641	0.715	0.034	1.465	Up	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)LLRGVFIVAAKR	0.001	0.020	0.001	0.012	2.526	1.337	0.012	1.911	Up	tr|I3N5Y9|I3N5Y9_ICTTR	Acetyl-CoA acyltransferase 2	ACAA2
AADQDLGPEAPPEGVLGALL	0.003	0.026	0.000	0.009	0.230	-2.118	0.009	2.036	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LQGFLVFH	0.000	0.007	0.001	0.011	3.172	1.665	0.007	2.131	Up	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
PYQYPAL	0.003	0.026	0.000	0.009	2.936	1.554	0.009	2.036	Up	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
Q(-17.03)EDAELQP	0.001	0.020	0.002	0.015	0.407	-1.298	0.015	1.836	Down	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
S(+42.01)ILKIHAREIFD	0.005	0.031	0.004	0.026	2.529	1.339	0.026	1.586	Up	tr|I3MIE7|I3MIE7_ICTTR	2-phospho-D-glycerate hydro-lyase	ENO1
SIGRFFG	0.002	0.026	0.001	0.012	4.276	2.096	0.012	1.911	Up	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIYPAPQVS	0.004	0.029	0.002	0.020	3.369	1.753	0.020	1.705	Up	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SLDKFLA	0.000	0.012	0.001	0.011	2.929	1.550	0.011	1.969	Up	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLFVSNHAY	0.001	0.015	0.001	0.012	1.976	0.982	0.012	1.911	Up	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
TVVYGEPITA	0.000	0.010	0.000	0.009	5.379	2.427	0.009	2.036	Up	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TYFPHFDL	0.003	0.026	0.002	0.015	2.330	1.220	0.015	1.836	Up	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYFPHFDLSHG	0.000	0.009	0.000	0.009	4.017	2.006	0.009	2.053	Up	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYNFAVLKLMGRG	0.003	0.026	0.004	0.026	7.646	2.935	0.026	1.586	Up	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRGTKF	0.003	0.026	0.002	0.015	4.900	2.293	0.015	1.836	Up	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
VPPVQVSPLIKL	0.001	0.015	0.002	0.020	2.357	1.237	0.015	1.817	Up	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

August vs October

Full stat

Code

contrast = combo_list[[3]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: August over October"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
A(+42.01)AYKLVLIRH	0.211	0.316	0.190	0.288	0.670	-0.577	0.288	0.541	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHG	0.427	0.520	0.297	0.392	0.709	-0.495	0.392	0.407	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHGE	0.028	0.058	0.011	0.026	0.579	-0.789	0.026	1.588	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)GQAFRKFLPLFDRVLVER	0.067	0.123	0.113	0.196	0.621	-0.688	0.123	0.910	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
A(+42.01)LLRGVFIVAAKR	0.032	0.065	0.019	0.042	0.547	-0.870	0.042	1.377	tr|I3N5Y9|I3N5Y9_ICTTR	Acetyl-CoA acyltransferase 2	ACAA2
AADQDLGPEAPPEGVLGA	0.000	0.001	0.000	0.001	3.762	1.912	0.001	2.969	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.004	0.013	0.000	0.001	3.886	1.958	0.001	2.939	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALL	0.002	0.009	0.001	0.005	2.566	1.359	0.005	2.307	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALLRV	0.004	0.013	0.002	0.007	3.012	1.591	0.007	2.160	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AEALERMFL	0.087	0.154	0.161	0.251	0.578	-0.790	0.154	0.812	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
AFQKVVAGVANALSHKYH	0.308	0.400	0.340	0.433	0.865	-0.209	0.400	0.398	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
AFVLVLYDELKKVI	0.444	0.535	0.546	0.624	0.713	-0.488	0.535	0.272	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
ALNSVAYERNAMQNY	0.045	0.086	0.063	0.115	1.775	0.828	0.086	1.065	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
ALNSVAYERNAMQNYE	0.000	0.001	0.000	0.001	4.614	2.206	0.001	3.005	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
APIGLKAVVG	0.639	0.708	0.489	0.577	1.180	0.239	0.577	0.239	tr|A0A287D563|A0A287D563_ICTTR	Syntaxin binding protein 1	STXBP1
ASWTREPLE	0.000	0.000	0.000	0.001	5.688	2.508	0.000	4.024	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
ASWTREPLEE	0.000	0.000	0.000	0.001	5.148	2.364	0.000	3.556	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
DIDTAAKFIGAGAA	0.046	0.086	0.031	0.066	2.055	1.039	0.066	1.177	tr|I3MKX8|I3MKX8_ICTTR	ATP synthase lipid-binding protein	ATP5MC1
DILGKYVD	0.103	0.177	0.136	0.224	0.664	-0.592	0.177	0.751	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
EDEAAWSLDRTQQ	0.000	0.000	0.000	0.001	6.677	2.739	0.000	4.400	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
EIGDEENSAKFPI(-.98)	0.009	0.024	0.006	0.015	2.704	1.435	0.015	1.813	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
FLGEAYHHVPESQ	0.006	0.016	0.003	0.009	4.570	2.192	0.009	2.055	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.000	0.002	0.001	0.004	4.605	2.203	0.002	2.684	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLVFHSFGGG	0.335	0.426	0.297	0.392	1.620	0.696	0.392	0.407	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
GAAAQSLYIANHAY	0.735	0.792	0.863	0.879	0.965	-0.052	0.792	0.101	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
GAEALERMFL	0.021	0.043	0.050	0.097	0.571	-0.808	0.043	1.362	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
GAFVLVLYDELKKVI	0.927	0.961	0.863	0.879	0.888	-0.171	0.879	0.056	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
GASLKPEFVDIINAKQ	0.952	0.977	0.863	0.879	1.025	0.035	0.879	0.056	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
GGFMRGL	0.756	0.806	0.666	0.732	1.783	0.835	0.732	0.136	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GLQGFLVFH	0.073	0.132	0.063	0.115	0.487	-1.038	0.115	0.940	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
KVVAGVANALSHKYH	0.018	0.041	0.006	0.015	0.484	-1.047	0.015	1.813	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
LEDEAKELQ	0.971	0.977	1.000	1.000	1.087	0.121	0.977	0.010	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
LENPQPQAPA	0.001	0.006	0.000	0.001	6.103	2.609	0.001	3.182	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LENPQPQAPARRLLPP	0.001	0.004	0.000	0.001	4.470	2.160	0.001	2.939	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGVLFNPYYDPLQWKSSRFE	0.002	0.009	0.011	0.026	2.219	1.150	0.009	2.043	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LQGFLVFH	0.009	0.025	0.006	0.015	0.395	-1.342	0.015	1.813	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
M(+42.01)DVFMKGL	0.001	0.004	0.000	0.001	0.134	-2.901	0.001	3.182	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
MDELYPVEPEEEANGGEVL	0.001	0.003	0.001	0.005	3.244	1.698	0.003	2.457	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MDELYPVEPEEEANGGEVLA	0.009	0.025	0.014	0.034	2.786	1.478	0.025	1.607	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MQIFVKTL	0.508	0.599	0.730	0.779	1.119	0.163	0.599	0.223	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLT	0.576	0.658	0.666	0.732	1.296	0.374	0.658	0.182	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLTGK	0.150	0.230	0.161	0.251	1.489	0.575	0.230	0.637	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
PMFVVNTNVPRA	0.977	0.977	0.546	0.624	1.128	0.174	0.624	0.205	tr|I3N9F5|I3N9F5_ICTTR	Macrophage migration inhibitory factor	MIF
PVNFKLL	0.016	0.038	0.024	0.054	0.301	-1.730	0.038	1.421	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
PYQYPAL	0.002	0.008	0.002	0.007	0.221	-2.176	0.007	2.160	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
Q(-17.03)EDAELQP	0.000	0.000	0.000	0.001	11.310	3.500	0.000	6.185	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)EDAELQPR	0.002	0.008	0.000	0.002	5.637	2.495	0.002	2.747	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)YDRVAELDQLLHY	0.004	0.013	0.001	0.005	1.893	0.921	0.005	2.307	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPKPQQFFGLM(-.98)	0.004	0.013	0.003	0.009	2.914	1.543	0.009	2.055	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
RTLYGFGG	0.590	0.668	0.605	0.684	1.170	0.227	0.668	0.176	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
S(+42.01)DKPDMAEIEKFDK	0.698	0.759	0.730	0.779	1.107	0.146	0.759	0.120	tr|A0A287CVS2|A0A287CVS2_ICTTR	Thymosin beta	Tmsb4x
S(+42.01)ILKIHAREIFD	0.264	0.360	0.136	0.224	0.665	-0.589	0.224	0.650	tr|I3MIE7|I3MIE7_ICTTR	2-phospho-D-glycerate hydro-lyase	ENO1
SAMLIQKL	0.246	0.344	0.340	0.433	0.742	-0.431	0.344	0.464	tr|I3M435|I3M435_ICTTR	Acetyl-CoA acetyltransferase 1	ACAT1
SAVISLEGKPL	0.522	0.609	0.489	0.577	0.942	-0.087	0.577	0.239	tr|I3MY03|I3MY03_ICTTR	Cofilin, non-muscle isoform	CFL1
SESLFVSNHAY	0.021	0.043	0.031	0.066	0.743	-0.429	0.043	1.362	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SFFAVMGA	0.245	0.344	0.340	0.433	0.618	-0.695	0.344	0.464	tr|A0A287CVH5|A0A287CVH5_ICTTR	Polypyrimidine tract binding protein 2	PTBP2
SGFAAPFFIVRHQLLKK	0.222	0.327	0.222	0.324	0.476	-1.071	0.324	0.490	tr|A0A287CU43|A0A287CU43_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967835
SGFTSLLMERL	0.338	0.426	0.258	0.361	0.806	-0.311	0.361	0.442	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SGPFGQIFRPDNFVFGQ	0.090	0.157	0.113	0.196	0.762	-0.392	0.157	0.804	tr|I3NEP5|I3NEP5_ICTTR	Tubulin beta chain	TUBB2B
SGSAKVAFSAIRSTNH	0.018	0.041	0.003	0.009	2.586	1.371	0.009	2.055	tr|I3MWG7|I3MWG7_ICTTR	GST class-pi	GSTP1
SHLGGAVF	0.004	0.013	0.003	0.009	0.312	-1.683	0.009	2.055	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
SIGRFFG	0.133	0.216	0.222	0.324	0.860	-0.217	0.216	0.666	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGG	0.002	0.009	0.008	0.020	0.289	-1.791	0.009	2.048	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGGDRG	0.002	0.009	0.001	0.005	0.270	-1.887	0.005	2.307	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIYPAPQVS	0.976	0.977	0.730	0.779	2.656	1.409	0.779	0.108	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SLDKFLA	0.000	0.001	0.000	0.001	0.108	-3.212	0.001	3.182	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLDKFLASVSTVLTSKYR	0.006	0.016	0.006	0.015	0.310	-1.689	0.015	1.813	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLFVSNHAY	0.000	0.001	0.000	0.001	0.365	-1.454	0.001	3.183	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SLKPEFVDIINAKQ	0.496	0.591	0.297	0.392	0.801	-0.320	0.392	0.407	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
SLSAASPPMTEAGTPRRF	0.000	0.002	0.000	0.003	3.443	1.784	0.002	2.663	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SLYIANHAY	0.004	0.014	0.004	0.012	0.476	-1.071	0.012	1.906	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
SPEPEAAAAVPRRL	0.264	0.360	0.387	0.465	1.519	0.603	0.360	0.443	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SPQLEDEAKEL	0.000	0.002	0.000	0.001	3.420	1.774	0.001	2.939	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.000	0.002	0.000	0.003	4.150	2.053	0.002	2.818	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SSPETLISDLLMRESTENVPRTRLEDPSMW	0.001	0.004	0.000	0.003	5.748	2.523	0.003	2.600	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY
STLHLVLRLRGG	0.301	0.397	0.387	0.465	0.875	-0.193	0.397	0.401	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
SVLISLKQAPLVH	0.135	0.216	0.190	0.288	0.611	-0.711	0.216	0.666	tr|A0A287D1C0|A0A287D1C0_ICTTR	Clathrin light chain	CLTA
SVPRGEAAGAVQELARALAHLLEAERQE	0.001	0.007	0.000	0.003	2.962	1.566	0.003	2.600	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SVSTVLTSKYR	0.310	0.400	0.258	0.361	0.677	-0.563	0.361	0.442	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TAYAIYELAKA	0.046	0.086	0.040	0.080	0.606	-0.723	0.080	1.097	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TAYAIYELAKASFPKKQD	0.294	0.393	0.297	0.392	0.897	-0.156	0.392	0.407	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TDYLMKIL	0.111	0.189	0.136	0.224	0.436	-1.199	0.189	0.724	tr|I3MNL1|I3MNL1_ICTTR	Actin beta	ACTB
TGLQGFLVFH	0.131	0.216	0.077	0.137	1.115	0.157	0.137	0.864	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TGLQGFLVFHSFGGG	0.611	0.684	0.546	0.624	1.136	0.184	0.624	0.205	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
THYKLVPHQFAH	0.016	0.038	0.011	0.026	0.440	-1.185	0.026	1.588	tr|I3MGG0|I3MGG0_ICTTR	Cytochrome c oxidase polypeptide Vb	LOC101965209
TIDFPEFL	0.007	0.020	0.019	0.042	0.350	-1.516	0.020	1.690	tr|I3MRD3|I3MRD3_ICTTR	Calmodulin	CALM1
TLHLVLRLRGG	0.122	0.205	0.077	0.137	0.650	-0.622	0.137	0.864	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
TLSKIFKLGGKDSRSGSPMARR	0.245	0.344	0.387	0.465	0.700	-0.515	0.344	0.464	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
TLYGFGG	0.034	0.067	0.040	0.080	0.500	-1.001	0.067	1.171	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TPAVHASLDKFLA	0.285	0.385	0.297	0.392	0.772	-0.373	0.385	0.415	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPAVHASLDKFLASVSTVLTSKYR	0.198	0.299	0.387	0.465	0.979	-0.031	0.299	0.524	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPEAQAAFQKVVAGVANALSHKYH	0.014	0.035	0.040	0.080	0.302	-1.729	0.035	1.456	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
TSLLMERL	0.014	0.035	0.008	0.020	0.211	-2.246	0.020	1.694	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TTMIIDHVVPEPG	0.529	0.611	0.863	0.879	1.658	0.729	0.611	0.214	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TVVYGEPITA	0.004	0.013	0.006	0.015	0.225	-2.149	0.013	1.881	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TYFPHFDL	0.020	0.043	0.063	0.115	0.571	-0.808	0.043	1.365	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYFPHFDLSHG	0.145	0.225	0.222	0.324	0.785	-0.350	0.225	0.648	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYNFAVLKLMG	0.046	0.086	0.050	0.097	0.489	-1.032	0.086	1.065	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRG	0.354	0.440	0.258	0.361	0.962	-0.056	0.361	0.442	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRGTKF	0.406	0.499	0.387	0.465	1.748	0.806	0.465	0.332	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
VGRPEWWMDYQ	0.005	0.016	0.003	0.009	2.735	1.452	0.009	2.055	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.014	0.035	0.019	0.042	2.210	1.144	0.035	1.456	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGFG	0.854	0.894	0.796	0.841	0.972	-0.041	0.841	0.075	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGR	0.816	0.862	0.931	0.940	0.996	-0.006	0.862	0.064	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGRIG	0.139	0.220	0.161	0.251	1.309	0.388	0.220	0.658	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VPPVQVSPLIKL	0.682	0.749	0.666	0.732	1.321	0.402	0.732	0.136	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
VPPVQVSPLIKLGRY	0.241	0.344	0.161	0.251	0.778	-0.362	0.251	0.600	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
YGGFLRKYP	0.000	0.001	0.000	0.001	5.038	2.333	0.001	3.182	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFLRKYPK	0.000	0.002	0.000	0.002	3.252	1.701	0.002	2.747	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFMRF	0.001	0.006	0.001	0.005	4.244	2.086	0.005	2.307	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.000	0.001	0.000	0.001	4.407	2.140	0.001	3.182	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY(-.98)	0.000	0.001	0.000	0.001	11.042	3.465	0.001	3.081	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	status	Accession	Name	GN
AADQDLGPEAPPEGVLGA	0.000	0.001	0.000	0.001	3.762	1.912	0.001	2.969	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.004	0.013	0.000	0.001	3.886	1.958	0.001	2.939	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALL	0.002	0.009	0.001	0.005	2.566	1.359	0.005	2.307	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALLRV	0.004	0.013	0.002	0.007	3.012	1.591	0.007	2.160	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
ALNSVAYERNAMQNYE	0.000	0.001	0.000	0.001	4.614	2.206	0.001	3.005	Up	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
ASWTREPLE	0.000	0.000	0.000	0.001	5.688	2.508	0.000	4.024	Up	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
ASWTREPLEE	0.000	0.000	0.000	0.001	5.148	2.364	0.000	3.556	Up	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
EDEAAWSLDRTQQ	0.000	0.000	0.000	0.001	6.677	2.739	0.000	4.400	Up	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
EIGDEENSAKFPI(-.98)	0.009	0.024	0.006	0.015	2.704	1.435	0.015	1.813	Up	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
FLGEAYHHVPESQ	0.006	0.016	0.003	0.009	4.570	2.192	0.009	2.055	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.000	0.002	0.001	0.004	4.605	2.203	0.002	2.684	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
KVVAGVANALSHKYH	0.018	0.041	0.006	0.015	0.484	-1.047	0.015	1.813	Down	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
LENPQPQAPA	0.001	0.006	0.000	0.001	6.103	2.609	0.001	3.182	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LENPQPQAPARRLLPP	0.001	0.004	0.000	0.001	4.470	2.160	0.001	2.939	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGVLFNPYYDPLQWKSSRFE	0.002	0.009	0.011	0.026	2.219	1.150	0.009	2.043	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LQGFLVFH	0.009	0.025	0.006	0.015	0.395	-1.342	0.015	1.813	Down	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
M(+42.01)DVFMKGL	0.001	0.004	0.000	0.001	0.134	-2.901	0.001	3.182	Down	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
MDELYPVEPEEEANGGEVL	0.001	0.003	0.001	0.005	3.244	1.698	0.003	2.457	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MDELYPVEPEEEANGGEVLA	0.009	0.025	0.014	0.034	2.786	1.478	0.025	1.607	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
PYQYPAL	0.002	0.008	0.002	0.007	0.221	-2.176	0.007	2.160	Down	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
Q(-17.03)EDAELQP	0.000	0.000	0.000	0.001	11.310	3.500	0.000	6.185	Up	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)EDAELQPR	0.002	0.008	0.000	0.002	5.637	2.495	0.002	2.747	Up	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)YDRVAELDQLLHY	0.004	0.013	0.001	0.005	1.893	0.921	0.005	2.307	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPKPQQFFGLM(-.98)	0.004	0.013	0.003	0.009	2.914	1.543	0.009	2.055	Up	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
SGSAKVAFSAIRSTNH	0.018	0.041	0.003	0.009	2.586	1.371	0.009	2.055	Up	tr|I3MWG7|I3MWG7_ICTTR	GST class-pi	GSTP1
SHLGGAVF	0.004	0.013	0.003	0.009	0.312	-1.683	0.009	2.055	Down	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
SIGRFFGG	0.002	0.009	0.008	0.020	0.289	-1.791	0.009	2.048	Down	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGGDRG	0.002	0.009	0.001	0.005	0.270	-1.887	0.005	2.307	Down	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SLDKFLA	0.000	0.001	0.000	0.001	0.108	-3.212	0.001	3.182	Down	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLDKFLASVSTVLTSKYR	0.006	0.016	0.006	0.015	0.310	-1.689	0.015	1.813	Down	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLFVSNHAY	0.000	0.001	0.000	0.001	0.365	-1.454	0.001	3.183	Down	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SLSAASPPMTEAGTPRRF	0.000	0.002	0.000	0.003	3.443	1.784	0.002	2.663	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SLYIANHAY	0.004	0.014	0.004	0.012	0.476	-1.071	0.012	1.906	Down	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
SPQLEDEAKEL	0.000	0.002	0.000	0.001	3.420	1.774	0.001	2.939	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.000	0.002	0.000	0.003	4.150	2.053	0.002	2.818	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SSPETLISDLLMRESTENVPRTRLEDPSMW	0.001	0.004	0.000	0.003	5.748	2.523	0.003	2.600	Up	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY
SVPRGEAAGAVQELARALAHLLEAERQE	0.001	0.007	0.000	0.003	2.962	1.566	0.003	2.600	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
THYKLVPHQFAH	0.016	0.038	0.011	0.026	0.440	-1.185	0.026	1.588	Down	tr|I3MGG0|I3MGG0_ICTTR	Cytochrome c oxidase polypeptide Vb	LOC101965209
TIDFPEFL	0.007	0.020	0.019	0.042	0.350	-1.516	0.020	1.690	Down	tr|I3MRD3|I3MRD3_ICTTR	Calmodulin	CALM1
TSLLMERL	0.014	0.035	0.008	0.020	0.211	-2.246	0.020	1.694	Down	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TVVYGEPITA	0.004	0.013	0.006	0.015	0.225	-2.149	0.013	1.881	Down	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
VGRPEWWMDYQ	0.005	0.016	0.003	0.009	2.735	1.452	0.009	2.055	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.014	0.035	0.019	0.042	2.210	1.144	0.035	1.456	Up	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
YGGFLRKYP	0.000	0.001	0.000	0.001	5.038	2.333	0.001	3.182	Up	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFLRKYPK	0.000	0.002	0.000	0.002	3.252	1.701	0.002	2.747	Up	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFMRF	0.001	0.006	0.001	0.005	4.244	2.086	0.005	2.307	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.000	0.001	0.000	0.001	4.407	2.140	0.001	3.182	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY(-.98)	0.000	0.001	0.000	0.001	11.042	3.465	0.001	3.081	Up	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

August vs Torpor

Full stat

Code

contrast = combo_list[[4]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: August over Torpor"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
A(+42.01)AYKLVLIRH	0.892	0.934	0.941	0.994	0.941	-0.088	0.934	0.030	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHG	0.934	0.952	1.000	1.000	1.001	0.002	0.952	0.021	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHGE	0.181	0.548	0.067	0.360	1.569	0.649	0.360	0.444	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)GQAFRKFLPLFDRVLVER	0.058	0.361	0.067	0.360	1.534	0.617	0.360	0.444	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
A(+42.01)LLRGVFIVAAKR	0.251	0.583	0.230	0.572	1.361	0.444	0.572	0.243	tr|I3N5Y9|I3N5Y9_ICTTR	Acetyl-CoA acyltransferase 2	ACAA2
AADQDLGPEAPPEGVLGA	0.419	0.745	0.331	0.674	0.745	-0.425	0.674	0.171	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.498	0.775	0.710	0.904	1.176	0.234	0.775	0.111	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALL	0.011	0.239	0.002	0.061	0.382	-1.390	0.061	1.212	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALLRV	0.044	0.361	0.031	0.267	0.533	-0.907	0.267	0.573	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AEALERMFL	0.695	0.847	0.370	0.680	2.073	1.052	0.680	0.168	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
AFQKVVAGVANALSHKYH	0.820	0.899	0.824	0.951	1.089	0.123	0.899	0.046	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
AFVLVLYDELKKVI	0.454	0.775	0.456	0.719	1.135	0.182	0.719	0.143	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
ALNSVAYERNAMQNY	0.944	0.953	0.766	0.943	0.639	-0.645	0.943	0.025	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
ALNSVAYERNAMQNYE	0.417	0.745	0.552	0.824	0.933	-0.101	0.745	0.128	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
APIGLKAVVG	0.775	0.896	0.603	0.865	1.070	0.098	0.865	0.063	tr|A0A287D563|A0A287D563_ICTTR	Syntaxin binding protein 1	STXBP1
ASWTREPLE	0.380	0.740	0.412	0.699	0.819	-0.289	0.699	0.156	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
ASWTREPLEE	0.127	0.457	0.131	0.444	2.383	1.253	0.444	0.353	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
DIDTAAKFIGAGAA	0.482	0.775	0.882	0.978	1.084	0.117	0.775	0.111	tr|I3MKX8|I3MKX8_ICTTR	ATP synthase lipid-binding protein	ATP5MC1
DILGKYVD	0.439	0.768	0.412	0.699	1.409	0.494	0.699	0.156	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
EDEAAWSLDRTQQ	0.565	0.795	0.456	0.719	1.058	0.081	0.719	0.143	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
EIGDEENSAKFPI(-.98)	0.587	0.795	0.456	0.719	0.927	-0.109	0.719	0.143	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
FLGEAYHHVPESQ	0.119	0.457	0.230	0.572	1.459	0.545	0.457	0.340	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.141	0.463	0.095	0.410	1.302	0.381	0.410	0.387	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLVFHSFGGG	0.213	0.549	0.230	0.572	2.089	1.063	0.549	0.260	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
GAAAQSLYIANHAY	0.090	0.402	0.131	0.444	1.436	0.522	0.402	0.396	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
GAEALERMFL	0.529	0.784	0.766	0.943	1.013	0.019	0.784	0.106	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
GAFVLVLYDELKKVI	0.019	0.314	0.025	0.267	0.412	-1.280	0.267	0.573	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
GASLKPEFVDIINAKQ	0.689	0.847	0.882	0.978	1.184	0.244	0.847	0.072	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
GGFMRGL	0.510	0.778	0.370	0.680	0.689	-0.538	0.680	0.168	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GLQGFLVFH	0.570	0.795	0.261	0.609	0.921	-0.118	0.609	0.215	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
KVVAGVANALSHKYH	0.131	0.457	0.370	0.680	1.629	0.704	0.457	0.340	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
LEDEAKELQ	0.076	0.372	0.112	0.432	1.795	0.844	0.372	0.430	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
LENPQPQAPA	0.368	0.736	0.412	0.699	1.225	0.292	0.699	0.156	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LENPQPQAPARRLLPP	0.956	0.956	0.710	0.904	0.827	-0.274	0.904	0.044	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGVLFNPYYDPLQWKSSRFE	0.828	0.899	0.824	0.951	0.958	-0.062	0.899	0.046	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LQGFLVFH	0.270	0.593	0.412	0.699	1.424	0.510	0.593	0.227	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
M(+42.01)DVFMKGL	0.029	0.361	0.006	0.158	0.603	-0.729	0.158	0.800	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
MDELYPVEPEEEANGGEVL	0.010	0.239	0.012	0.199	0.468	-1.094	0.199	0.700	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MDELYPVEPEEEANGGEVLA	0.041	0.361	0.025	0.267	0.425	-1.234	0.267	0.573	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MQIFVKTL	0.033	0.361	0.012	0.199	2.126	1.088	0.199	0.700	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLT	0.357	0.726	0.503	0.761	1.424	0.510	0.726	0.139	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLTGK	0.393	0.740	0.230	0.572	1.653	0.725	0.572	0.243	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
PMFVVNTNVPRA	0.771	0.896	0.710	0.904	0.926	-0.110	0.896	0.048	tr|I3N9F5|I3N9F5_ICTTR	Macrophage migration inhibitory factor	MIF
PVNFKLL	0.090	0.402	0.046	0.306	1.490	0.576	0.306	0.514	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
PYQYPAL	0.052	0.361	0.046	0.306	1.751	0.808	0.306	0.514	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
Q(-17.03)EDAELQP	0.800	0.897	0.656	0.885	1.424	0.510	0.885	0.053	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)EDAELQPR	0.589	0.795	0.152	0.501	0.541	-0.886	0.501	0.301	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)YDRVAELDQLLHY	0.069	0.370	0.080	0.375	0.682	-0.553	0.370	0.432	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPKPQQFFGLM(-.98)	0.064	0.370	0.046	0.306	1.706	0.771	0.306	0.514	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
RTLYGFGG	0.493	0.775	0.656	0.885	1.188	0.249	0.775	0.111	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
S(+42.01)DKPDMAEIEKFDK	0.670	0.834	0.603	0.865	1.098	0.135	0.834	0.079	tr|A0A287CVS2|A0A287CVS2_ICTTR	Thymosin beta	Tmsb4x
S(+42.01)ILKIHAREIFD	0.152	0.473	0.175	0.517	1.414	0.500	0.473	0.325	tr|I3MIE7|I3MIE7_ICTTR	2-phospho-D-glycerate hydro-lyase	ENO1
SAMLIQKL	0.479	0.775	0.656	0.885	0.897	-0.156	0.775	0.111	tr|I3M435|I3M435_ICTTR	Acetyl-CoA acetyltransferase 1	ACAT1
SAVISLEGKPL	0.935	0.952	0.882	0.978	1.014	0.020	0.952	0.021	tr|I3MY03|I3MY03_ICTTR	Cofilin, non-muscle isoform	CFL1
SESLFVSNHAY	0.216	0.549	0.261	0.609	1.218	0.284	0.549	0.260	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SFFAVMGA	0.345	0.717	0.503	0.761	0.552	-0.858	0.717	0.145	tr|A0A287CVH5|A0A287CVH5_ICTTR	Polypyrimidine tract binding protein 2	PTBP2
SGFAAPFFIVRHQLLKK	0.624	0.818	0.824	0.951	1.063	0.089	0.818	0.087	tr|A0A287CU43|A0A287CU43_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967835
SGFTSLLMERL	0.187	0.548	0.295	0.647	0.450	-1.152	0.548	0.261	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SGPFGQIFRPDNFVFGQ	0.098	0.420	0.038	0.305	0.846	-0.241	0.305	0.516	tr|I3NEP5|I3NEP5_ICTTR	Tubulin beta chain	TUBB2B
SGSAKVAFSAIRSTNH	0.514	0.778	0.456	0.719	0.695	-0.525	0.719	0.143	tr|I3MWG7|I3MWG7_ICTTR	GST class-pi	GSTP1
SHLGGAVF	0.776	0.896	0.503	0.761	1.480	0.565	0.761	0.119	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
SIGRFFG	0.151	0.473	0.201	0.564	1.491	0.576	0.473	0.325	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGG	0.055	0.361	0.067	0.360	4.057	2.020	0.360	0.444	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGGDRG	0.074	0.372	0.080	0.375	1.817	0.862	0.372	0.430	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIYPAPQVS	0.010	0.239	0.010	0.199	3.132	1.647	0.199	0.700	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SLDKFLA	0.645	0.818	0.766	0.943	1.180	0.239	0.818	0.087	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLDKFLASVSTVLTSKYR	0.857	0.905	1.000	1.000	1.039	0.055	0.905	0.043	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLFVSNHAY	0.196	0.548	0.175	0.517	1.297	0.375	0.517	0.287	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SLKPEFVDIINAKQ	0.318	0.686	0.370	0.680	1.149	0.201	0.680	0.168	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
SLSAASPPMTEAGTPRRF	0.066	0.370	0.056	0.350	0.498	-1.005	0.350	0.456	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SLYIANHAY	0.586	0.795	0.824	0.951	1.192	0.253	0.795	0.100	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
SPEPEAAAAVPRRL	0.021	0.314	0.020	0.267	0.369	-1.438	0.267	0.573	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SPQLEDEAKEL	0.260	0.583	0.112	0.432	0.658	-0.604	0.432	0.364	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.539	0.784	1.000	1.000	0.960	-0.059	0.784	0.106	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SSPETLISDLLMRESTENVPRTRLEDPSMW	0.596	0.795	0.710	0.904	0.886	-0.175	0.795	0.100	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY
STLHLVLRLRGG	0.022	0.314	0.031	0.267	1.551	0.633	0.267	0.573	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
SVLISLKQAPLVH	0.730	0.870	0.882	0.978	1.110	0.151	0.870	0.060	tr|A0A287D1C0|A0A287D1C0_ICTTR	Clathrin light chain	CLTA
SVPRGEAAGAVQELARALAHLLEAERQE	0.790	0.897	0.656	0.885	0.856	-0.224	0.885	0.053	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SVSTVLTSKYR	0.838	0.899	0.941	0.994	1.187	0.248	0.899	0.046	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TAYAIYELAKA	0.045	0.361	0.031	0.267	1.676	0.745	0.267	0.573	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TAYAIYELAKASFPKKQD	0.536	0.784	0.941	0.994	1.002	0.003	0.784	0.106	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TDYLMKIL	0.800	0.897	1.000	1.000	0.941	-0.087	0.897	0.047	tr|I3MNL1|I3MNL1_ICTTR	Actin beta	ACTB
TGLQGFLVFH	0.213	0.549	0.412	0.699	1.730	0.791	0.549	0.260	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TGLQGFLVFHSFGGG	0.650	0.818	0.824	0.951	1.449	0.535	0.818	0.087	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
THYKLVPHQFAH	0.229	0.554	0.370	0.680	1.336	0.417	0.554	0.256	tr|I3MGG0|I3MGG0_ICTTR	Cytochrome c oxidase polypeptide Vb	LOC101965209
TIDFPEFL	0.843	0.899	0.261	0.609	0.964	-0.053	0.609	0.215	tr|I3MRD3|I3MRD3_ICTTR	Calmodulin	CALM1
TLHLVLRLRGG	0.233	0.554	0.175	0.517	1.782	0.833	0.517	0.287	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
TLSKIFKLGGKDSRSGSPMARR	0.494	0.775	0.824	0.951	1.057	0.080	0.775	0.111	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
TLYGFGG	0.259	0.583	0.331	0.674	1.169	0.225	0.583	0.234	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TPAVHASLDKFLA	0.393	0.740	0.230	0.572	1.058	0.081	0.572	0.243	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPAVHASLDKFLASVSTVLTSKYR	0.575	0.795	0.941	0.994	1.770	0.824	0.795	0.100	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPEAQAAFQKVVAGVANALSHKYH	0.136	0.462	0.295	0.647	1.500	0.585	0.462	0.335	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
TSLLMERL	0.476	0.775	0.456	0.719	0.716	-0.481	0.719	0.143	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TTMIIDHVVPEPG	0.412	0.745	0.131	0.444	1.782	0.833	0.444	0.353	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TVVYGEPITA	0.048	0.361	0.112	0.432	4.580	2.195	0.361	0.443	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TYFPHFDL	0.129	0.457	0.175	0.517	3.639	1.863	0.457	0.340	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYFPHFDLSHG	0.111	0.445	0.131	0.444	3.971	1.990	0.444	0.353	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYNFAVLKLMG	0.904	0.937	1.000	1.000	0.906	-0.142	0.937	0.028	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRG	0.048	0.361	0.080	0.375	3.842	1.942	0.361	0.443	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRGTKF	0.104	0.431	0.095	0.410	2.172	1.119	0.410	0.387	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
VGRPEWWMDYQ	0.632	0.818	0.603	0.865	0.653	-0.616	0.818	0.087	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.496	0.775	0.941	0.994	0.884	-0.178	0.775	0.111	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGFG	0.191	0.548	0.331	0.674	0.852	-0.232	0.548	0.261	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGR	0.227	0.554	0.201	0.564	1.302	0.381	0.554	0.256	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGRIG	0.727	0.870	0.710	0.904	0.960	-0.060	0.870	0.060	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VPPVQVSPLIKL	0.002	0.094	0.002	0.061	2.332	1.221	0.061	1.212	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
VPPVQVSPLIKLGRY	0.000	0.012	0.000	0.005	2.768	1.469	0.005	2.273	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
YGGFLRKYP	0.827	0.899	1.000	1.000	0.766	-0.385	0.899	0.046	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFLRKYPK	0.396	0.740	0.370	0.680	1.148	0.199	0.680	0.168	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFMRF	0.647	0.818	0.656	0.885	1.046	0.065	0.818	0.087	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.205	0.549	0.295	0.647	1.489	0.574	0.549	0.260	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY(-.98)	0.346	0.717	0.331	0.674	1.000	0.001	0.674	0.171	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	status	Accession	Name	GN
VPPVQVSPLIKLGRY	0	0.012	0	0.005	2.768	1.469	0.005	2.273	Up	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

IBA vs March

Full stat

Code

contrast = combo_list[[5]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: IBA over March"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
A(+42.01)AYKLVLIRH	0.165	0.264	0.195	0.307	2.144	1.101	0.264	0.579	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHG	0.068	0.166	0.038	0.101	1.395	0.480	0.101	0.995	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHGE	0.084	0.178	0.083	0.175	1.292	0.369	0.175	0.756	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)GQAFRKFLPLFDRVLVER	0.254	0.370	0.328	0.432	1.263	0.337	0.370	0.432	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
A(+42.01)LLRGVFIVAAKR	0.005	0.029	0.007	0.034	2.187	1.129	0.029	1.536	tr|I3N5Y9|I3N5Y9_ICTTR	Acetyl-CoA acyltransferase 2	ACAA2
AADQDLGPEAPPEGVLGA	0.141	0.235	0.234	0.346	0.405	-1.303	0.235	0.629	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.664	0.751	0.645	0.709	0.552	-0.858	0.709	0.150	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALL	0.004	0.026	0.001	0.012	0.248	-2.012	0.012	1.935	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALLRV	0.076	0.174	0.021	0.064	0.427	-1.228	0.064	1.192	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AEALERMFL	0.029	0.091	0.038	0.101	2.310	1.208	0.091	1.042	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
AFQKVVAGVANALSHKYH	0.012	0.050	0.021	0.064	2.610	1.384	0.050	1.304	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
AFVLVLYDELKKVI	0.199	0.305	0.105	0.206	2.041	1.029	0.206	0.686	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
ALNSVAYERNAMQNY	0.102	0.196	0.161	0.272	0.610	-0.713	0.196	0.708	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
ALNSVAYERNAMQNYE	0.000	0.014	0.000	0.012	0.225	-2.154	0.012	1.935	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
APIGLKAVVG	0.117	0.204	0.195	0.307	1.396	0.482	0.204	0.691	tr|A0A287D563|A0A287D563_ICTTR	Syntaxin binding protein 1	STXBP1
ASWTREPLE	0.081	0.178	0.065	0.146	0.617	-0.697	0.146	0.837	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
ASWTREPLEE	0.958	0.958	0.645	0.709	0.836	-0.258	0.709	0.150	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
DIDTAAKFIGAGAA	0.318	0.434	0.442	0.550	1.873	0.905	0.434	0.363	tr|I3MKX8|I3MKX8_ICTTR	ATP synthase lipid-binding protein	ATP5MC1
DILGKYVD	0.676	0.755	1.000	1.000	0.805	-0.313	0.755	0.122	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
EDEAAWSLDRTQQ	0.062	0.161	0.065	0.146	0.528	-0.921	0.146	0.837	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
EIGDEENSAKFPI(-.98)	0.362	0.476	0.442	0.550	0.825	-0.278	0.476	0.322	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
FLGEAYHHVPESQ	0.078	0.174	0.105	0.206	0.468	-1.095	0.174	0.759	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.009	0.045	0.002	0.015	0.257	-1.962	0.015	1.826	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLVFHSFGGG	0.420	0.516	0.645	0.709	1.272	0.348	0.516	0.287	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
GAAAQSLYIANHAY	0.111	0.201	0.161	0.272	2.854	1.513	0.201	0.696	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
GAEALERMFL	0.002	0.019	0.002	0.015	3.159	1.659	0.015	1.826	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
GAFVLVLYDELKKVI	0.901	0.934	0.959	0.977	1.075	0.104	0.934	0.030	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
GASLKPEFVDIINAKQ	0.444	0.534	0.721	0.769	0.885	-0.176	0.534	0.272	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
GGFMRGL	0.383	0.486	0.234	0.346	0.509	-0.973	0.346	0.461	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GLQGFLVFH	0.006	0.032	0.005	0.029	3.026	1.597	0.029	1.537	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
KVVAGVANALSHKYH	0.917	0.940	0.878	0.911	1.632	0.706	0.911	0.040	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
LEDEAKELQ	0.074	0.174	0.105	0.206	0.447	-1.163	0.174	0.759	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
LENPQPQAPA	0.012	0.050	0.021	0.064	0.335	-1.576	0.050	1.304	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LENPQPQAPARRLLPP	0.588	0.685	0.645	0.709	0.799	-0.324	0.685	0.164	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGVLFNPYYDPLQWKSSRFE	0.000	0.009	0.001	0.012	0.309	-1.697	0.009	2.048	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LQGFLVFH	0.010	0.045	0.010	0.043	2.462	1.300	0.043	1.365	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
M(+42.01)DVFMKGL	0.015	0.057	0.021	0.064	1.993	0.995	0.057	1.241	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
MDELYPVEPEEEANGGEVL	0.045	0.127	0.015	0.055	0.398	-1.329	0.055	1.259	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MDELYPVEPEEEANGGEVLA	0.004	0.027	0.010	0.043	0.244	-2.036	0.027	1.577	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MQIFVKTL	0.822	0.868	0.721	0.769	0.844	-0.245	0.769	0.114	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLT	0.140	0.235	0.195	0.307	0.747	-0.421	0.235	0.629	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLTGK	0.781	0.841	0.574	0.662	1.208	0.273	0.662	0.179	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
PMFVVNTNVPRA	0.067	0.166	0.010	0.043	1.883	0.913	0.043	1.365	tr|I3N9F5|I3N9F5_ICTTR	Macrophage migration inhibitory factor	MIF
PVNFKLL	0.004	0.027	0.007	0.034	3.163	1.661	0.027	1.577	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
PYQYPAL	0.001	0.016	0.002	0.015	3.259	1.704	0.015	1.826	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
Q(-17.03)EDAELQP	0.000	0.004	0.000	0.012	0.205	-2.290	0.004	2.405	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)EDAELQPR	0.113	0.201	0.328	0.432	0.610	-0.714	0.201	0.696	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)YDRVAELDQLLHY	0.001	0.016	0.002	0.015	0.411	-1.282	0.015	1.826	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPKPQQFFGLM(-.98)	0.236	0.357	0.382	0.487	0.804	-0.315	0.357	0.448	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
RTLYGFGG	0.086	0.178	0.083	0.175	1.510	0.594	0.175	0.756	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
S(+42.01)DKPDMAEIEKFDK	0.311	0.430	0.382	0.487	0.808	-0.308	0.430	0.367	tr|A0A287CVS2|A0A287CVS2_ICTTR	Thymosin beta	Tmsb4x
S(+42.01)ILKIHAREIFD	0.037	0.110	0.007	0.034	2.045	1.032	0.034	1.468	tr|I3MIE7|I3MIE7_ICTTR	2-phospho-D-glycerate hydro-lyase	ENO1
SAMLIQKL	0.704	0.773	0.574	0.662	1.393	0.478	0.662	0.179	tr|I3M435|I3M435_ICTTR	Acetyl-CoA acetyltransferase 1	ACAT1
SAVISLEGKPL	0.171	0.270	0.050	0.124	1.538	0.621	0.124	0.906	tr|I3MY03|I3MY03_ICTTR	Cofilin, non-muscle isoform	CFL1
SESLFVSNHAY	0.085	0.178	0.130	0.236	1.361	0.444	0.178	0.750	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SFFAVMGA	0.606	0.700	0.878	0.911	0.984	-0.024	0.700	0.155	tr|A0A287CVH5|A0A287CVH5_ICTTR	Polypyrimidine tract binding protein 2	PTBP2
SGFAAPFFIVRHQLLKK	0.026	0.091	0.028	0.081	2.938	1.555	0.081	1.093	tr|A0A287CU43|A0A287CU43_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967835
SGFTSLLMERL	0.148	0.241	0.050	0.124	2.427	1.279	0.124	0.906	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SGPFGQIFRPDNFVFGQ	0.857	0.898	0.645	0.709	1.378	0.463	0.709	0.150	tr|I3NEP5|I3NEP5_ICTTR	Tubulin beta chain	TUBB2B
SGSAKVAFSAIRSTNH	0.099	0.194	0.083	0.175	0.618	-0.695	0.175	0.756	tr|I3MWG7|I3MWG7_ICTTR	GST class-pi	GSTP1
SHLGGAVF	0.110	0.201	0.161	0.272	2.188	1.130	0.201	0.696	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
SIGRFFG	0.000	0.009	0.001	0.012	4.000	2.000	0.009	2.048	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGG	0.008	0.039	0.021	0.064	4.069	2.025	0.039	1.410	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGGDRG	0.351	0.470	0.328	0.432	1.116	0.159	0.432	0.364	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIYPAPQVS	0.027	0.091	0.028	0.081	2.272	1.184	0.081	1.093	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SLDKFLA	0.042	0.121	0.028	0.081	1.931	0.949	0.081	1.093	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLDKFLASVSTVLTSKYR	0.478	0.570	0.505	0.615	1.234	0.303	0.570	0.244	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLFVSNHAY	0.001	0.016	0.001	0.015	1.871	0.904	0.015	1.826	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SLKPEFVDIINAKQ	0.763	0.830	0.382	0.487	1.301	0.379	0.487	0.313	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
SLSAASPPMTEAGTPRRF	0.681	0.755	0.328	0.432	0.807	-0.309	0.432	0.364	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SLYIANHAY	0.075	0.174	0.105	0.206	1.584	0.664	0.174	0.759	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
SPEPEAAAAVPRRL	0.245	0.361	0.279	0.395	1.769	0.823	0.361	0.442	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SPQLEDEAKEL	0.093	0.190	0.130	0.236	0.562	-0.831	0.190	0.722	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.057	0.152	0.065	0.146	0.450	-1.153	0.146	0.837	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SSPETLISDLLMRESTENVPRTRLEDPSMW	0.939	0.947	0.574	0.662	0.653	-0.615	0.662	0.179	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY
STLHLVLRLRGG	0.631	0.721	0.959	0.977	0.850	-0.235	0.721	0.142	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
SVLISLKQAPLVH	0.112	0.201	0.195	0.307	1.482	0.567	0.201	0.696	tr|A0A287D1C0|A0A287D1C0_ICTTR	Clathrin light chain	CLTA
SVPRGEAAGAVQELARALAHLLEAERQE	0.118	0.204	0.195	0.307	0.649	-0.624	0.204	0.691	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SVSTVLTSKYR	0.391	0.486	0.234	0.346	3.003	1.586	0.346	0.461	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TAYAIYELAKA	0.103	0.196	0.065	0.146	1.874	0.906	0.146	0.837	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TAYAIYELAKASFPKKQD	0.294	0.412	0.234	0.346	1.416	0.502	0.346	0.461	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TDYLMKIL	0.001	0.016	0.003	0.021	3.646	1.866	0.016	1.804	tr|I3MNL1|I3MNL1_ICTTR	Actin beta	ACTB
TGLQGFLVFH	0.004	0.027	0.007	0.034	4.256	2.090	0.027	1.577	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TGLQGFLVFHSFGGG	0.809	0.863	0.574	0.662	1.127	0.172	0.662	0.179	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
THYKLVPHQFAH	0.923	0.940	0.878	0.911	1.151	0.203	0.911	0.040	tr|I3MGG0|I3MGG0_ICTTR	Cytochrome c oxidase polypeptide Vb	LOC101965209
TIDFPEFL	0.096	0.192	0.130	0.236	2.499	1.321	0.192	0.717	tr|I3MRD3|I3MRD3_ICTTR	Calmodulin	CALM1
TLHLVLRLRGG	0.184	0.286	0.328	0.432	0.575	-0.798	0.286	0.544	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
TLSKIFKLGGKDSRSGSPMARR	0.245	0.361	0.279	0.395	1.441	0.527	0.361	0.442	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
TLYGFGG	0.352	0.470	0.279	0.395	1.306	0.385	0.395	0.403	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TPAVHASLDKFLA	0.292	0.412	0.161	0.272	1.613	0.690	0.272	0.565	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPAVHASLDKFLASVSTVLTSKYR	0.383	0.486	0.328	0.432	1.615	0.692	0.432	0.364	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPEAQAAFQKVVAGVANALSHKYH	0.037	0.110	0.065	0.146	2.061	1.043	0.110	0.958	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
TSLLMERL	0.029	0.091	0.021	0.064	4.002	2.001	0.064	1.192	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TTMIIDHVVPEPG	0.146	0.240	0.234	0.346	2.236	1.161	0.240	0.619	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TVVYGEPITA	0.010	0.045	0.007	0.034	3.234	1.693	0.034	1.468	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TYFPHFDL	0.001	0.016	0.002	0.015	2.115	1.081	0.015	1.826	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYFPHFDLSHG	0.003	0.021	0.005	0.029	3.102	1.633	0.021	1.687	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYNFAVLKLMG	0.027	0.091	0.015	0.055	2.535	1.342	0.055	1.259	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRG	0.002	0.018	0.003	0.021	10.192	3.349	0.018	1.738	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRGTKF	0.047	0.129	0.130	0.236	2.786	1.478	0.129	0.890	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
VGRPEWWMDYQ	0.001	0.016	0.001	0.012	0.287	-1.801	0.012	1.935	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.010	0.045	0.015	0.055	0.561	-0.834	0.045	1.347	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGFG	0.065	0.165	0.050	0.124	3.023	1.596	0.124	0.906	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGR	0.437	0.532	1.000	1.000	1.112	0.154	0.532	0.274	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGRIG	0.288	0.412	0.130	0.236	1.672	0.741	0.236	0.628	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VPPVQVSPLIKL	0.389	0.486	0.574	0.662	1.157	0.211	0.486	0.313	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
VPPVQVSPLIKLGRY	0.029	0.091	0.038	0.101	2.188	1.130	0.091	1.042	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
YGGFLRKYP	0.007	0.039	0.002	0.015	0.298	-1.745	0.015	1.826	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFLRKYPK	0.384	0.486	0.505	0.615	0.648	-0.627	0.486	0.313	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFMRF	0.013	0.050	0.010	0.043	0.450	-1.151	0.043	1.365	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.002	0.018	0.001	0.015	0.397	-1.331	0.015	1.826	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY(-.98)	0.560	0.661	0.721	0.769	0.934	-0.099	0.661	0.180	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	status	Accession	Name	GN
A(+42.01)LLRGVFIVAAKR	0.005	0.029	0.007	0.034	2.187	1.129	0.029	1.536	Up	tr|I3N5Y9|I3N5Y9_ICTTR	Acetyl-CoA acyltransferase 2	ACAA2
AADQDLGPEAPPEGVLGALL	0.004	0.026	0.001	0.012	0.248	-2.012	0.012	1.935	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
ALNSVAYERNAMQNYE	0.000	0.014	0.000	0.012	0.225	-2.154	0.012	1.935	Down	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
FLGEAYHHVPESQRD	0.009	0.045	0.002	0.015	0.257	-1.962	0.015	1.826	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GAEALERMFL	0.002	0.019	0.002	0.015	3.159	1.659	0.015	1.826	Up	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
GLQGFLVFH	0.006	0.032	0.005	0.029	3.026	1.597	0.029	1.537	Up	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
LGVLFNPYYDPLQWKSSRFE	0.000	0.009	0.001	0.012	0.309	-1.697	0.009	2.048	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LQGFLVFH	0.010	0.045	0.010	0.043	2.462	1.300	0.043	1.365	Up	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
MDELYPVEPEEEANGGEVLA	0.004	0.027	0.010	0.043	0.244	-2.036	0.027	1.577	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
PVNFKLL	0.004	0.027	0.007	0.034	3.163	1.661	0.027	1.577	Up	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
PYQYPAL	0.001	0.016	0.002	0.015	3.259	1.704	0.015	1.826	Up	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
Q(-17.03)EDAELQP	0.000	0.004	0.000	0.012	0.205	-2.290	0.004	2.405	Down	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)YDRVAELDQLLHY	0.001	0.016	0.002	0.015	0.411	-1.282	0.015	1.826	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SIGRFFG	0.000	0.009	0.001	0.012	4.000	2.000	0.009	2.048	Up	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SLFVSNHAY	0.001	0.016	0.001	0.015	1.871	0.904	0.015	1.826	Up	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
TDYLMKIL	0.001	0.016	0.003	0.021	3.646	1.866	0.016	1.804	Up	tr|I3MNL1|I3MNL1_ICTTR	Actin beta	ACTB
TGLQGFLVFH	0.004	0.027	0.007	0.034	4.256	2.090	0.027	1.577	Up	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TVVYGEPITA	0.010	0.045	0.007	0.034	3.234	1.693	0.034	1.468	Up	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TYFPHFDL	0.001	0.016	0.002	0.015	2.115	1.081	0.015	1.826	Up	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYFPHFDLSHG	0.003	0.021	0.005	0.029	3.102	1.633	0.021	1.687	Up	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYNFAVLKLMGRG	0.002	0.018	0.003	0.021	10.192	3.349	0.018	1.738	Up	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
VGRPEWWMDYQ	0.001	0.016	0.001	0.012	0.287	-1.801	0.012	1.935	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFLRKYP	0.007	0.039	0.002	0.015	0.298	-1.745	0.015	1.826	Down	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFMRF	0.013	0.050	0.010	0.043	0.450	-1.151	0.043	1.365	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.002	0.018	0.001	0.015	0.397	-1.331	0.015	1.826	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

IBA vs October

Full stat

Code

contrast = combo_list[[6]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: IBA over October"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
A(+42.01)AYKLVLIRH	0.772	0.824	0.888	0.905	0.910	-0.136	0.824	0.084	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHG	0.085	0.155	0.074	0.146	0.614	-0.703	0.146	0.835	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHGE	0.003	0.020	0.001	0.009	0.456	-1.134	0.009	2.036	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)GQAFRKFLPLFDRVLVER	0.094	0.168	0.139	0.222	0.485	-1.044	0.168	0.774	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
A(+42.01)LLRGVFIVAAKR	0.027	0.073	0.015	0.050	0.474	-1.078	0.050	1.300	tr|I3N5Y9|I3N5Y9_ICTTR	Acetyl-CoA acyltransferase 2	ACAA2
AADQDLGPEAPPEGVLGA	0.010	0.038	0.011	0.043	2.401	1.264	0.038	1.415	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.075	0.147	0.059	0.125	1.472	0.557	0.125	0.902	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALL	0.001	0.011	0.002	0.010	2.761	1.465	0.010	1.987	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALLRV	0.008	0.033	0.004	0.018	2.967	1.569	0.018	1.744	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AEALERMFL	0.056	0.113	0.114	0.193	0.528	-0.921	0.113	0.947	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
AFQKVVAGVANALSHKYH	0.377	0.472	0.606	0.659	0.973	-0.040	0.472	0.326	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
AFVLVLYDELKKVI	0.328	0.433	0.541	0.632	1.412	0.498	0.433	0.364	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
ALNSVAYERNAMQNY	0.778	0.824	0.673	0.718	1.202	0.266	0.718	0.144	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
ALNSVAYERNAMQNYE	0.102	0.174	0.200	0.276	1.719	0.782	0.174	0.760	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
APIGLKAVVG	0.818	0.856	0.888	0.905	1.078	0.108	0.856	0.067	tr|A0A287D563|A0A287D563_ICTTR	Syntaxin binding protein 1	STXBP1
ASWTREPLE	0.000	0.005	0.001	0.009	3.077	1.621	0.005	2.285	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
ASWTREPLEE	0.049	0.103	0.027	0.071	2.205	1.141	0.071	1.147	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
DIDTAAKFIGAGAA	0.043	0.094	0.059	0.125	2.024	1.017	0.094	1.027	tr|I3MKX8|I3MKX8_ICTTR	ATP synthase lipid-binding protein	ATP5MC1
DILGKYVD	0.188	0.268	0.093	0.170	0.303	-1.723	0.170	0.769	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
EDEAAWSLDRTQQ	0.001	0.008	0.001	0.009	3.345	1.742	0.008	2.086	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
EIGDEENSAKFPI(-.98)	0.035	0.088	0.036	0.092	1.973	0.981	0.088	1.054	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
FLGEAYHHVPESQ	0.252	0.344	0.423	0.527	1.653	0.725	0.344	0.463	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.150	0.230	0.114	0.193	1.492	0.577	0.193	0.714	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLVFHSFGGG	0.416	0.501	0.423	0.527	0.781	-0.356	0.501	0.300	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
GAAAQSLYIANHAY	0.754	0.820	0.606	0.659	0.862	-0.214	0.659	0.181	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
GAEALERMFL	0.078	0.148	0.167	0.246	0.885	-0.175	0.148	0.830	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
GAFVLVLYDELKKVI	0.958	0.984	0.888	0.905	0.874	-0.194	0.905	0.044	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
GASLKPEFVDIINAKQ	0.309	0.412	0.541	0.632	0.848	-0.238	0.412	0.385	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
GGFMRGL	0.372	0.472	0.236	0.322	0.950	-0.074	0.322	0.492	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GLQGFLVFH	0.239	0.331	0.167	0.246	0.749	-0.417	0.246	0.608	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
KVVAGVANALSHKYH	0.011	0.039	0.008	0.033	0.386	-1.373	0.033	1.485	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
LEDEAKELQ	0.025	0.071	0.027	0.071	0.347	-1.526	0.071	1.149	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
LENPQPQAPA	0.015	0.045	0.015	0.050	2.117	1.082	0.045	1.345	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LENPQPQAPARRLLPP	0.005	0.026	0.002	0.010	2.550	1.350	0.010	1.987	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGVLFNPYYDPLQWKSSRFE	0.455	0.542	0.277	0.369	1.210	0.275	0.369	0.433	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LQGFLVFH	0.048	0.103	0.059	0.125	0.306	-1.707	0.103	0.987	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
M(+42.01)DVFMKGL	0.004	0.024	0.000	0.009	0.236	-2.082	0.009	2.036	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
MDELYPVEPEEEANGGEVL	0.017	0.050	0.015	0.050	2.103	1.072	0.050	1.300	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MDELYPVEPEEEANGGEVLA	0.275	0.371	0.370	0.477	1.433	0.519	0.371	0.431	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MQIFVKTL	0.032	0.084	0.046	0.111	0.365	-1.452	0.084	1.077	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLT	0.039	0.088	0.074	0.146	0.570	-0.810	0.088	1.054	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLTGK	0.697	0.773	0.606	0.659	0.916	-0.126	0.659	0.181	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
PMFVVNTNVPRA	0.989	0.992	0.606	0.659	1.143	0.193	0.659	0.181	tr|I3N9F5|I3N9F5_ICTTR	Macrophage migration inhibitory factor	MIF
PVNFKLL	0.020	0.059	0.074	0.146	0.580	-0.786	0.059	1.231	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
PYQYPAL	0.001	0.011	0.002	0.010	0.246	-2.026	0.010	1.987	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
Q(-17.03)EDAELQP	0.000	0.001	0.000	0.009	5.688	2.508	0.001	3.262	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)EDAELQPR	0.001	0.013	0.002	0.014	3.511	1.812	0.013	1.889	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)YDRVAELDQLLHY	0.123	0.196	0.046	0.111	1.363	0.447	0.111	0.956	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPKPQQFFGLM(-.98)	0.589	0.671	0.541	0.632	1.007	0.010	0.632	0.200	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
RTLYGFGG	0.505	0.592	0.541	0.632	0.903	-0.147	0.592	0.228	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
S(+42.01)DKPDMAEIEKFDK	0.507	0.592	0.606	0.659	0.846	-0.240	0.592	0.228	tr|A0A287CVS2|A0A287CVS2_ICTTR	Thymosin beta	Tmsb4x
S(+42.01)ILKIHAREIFD	0.146	0.227	0.059	0.125	0.537	-0.896	0.125	0.902	tr|I3MIE7|I3MIE7_ICTTR	2-phospho-D-glycerate hydro-lyase	ENO1
SAMLIQKL	0.013	0.043	0.027	0.071	0.544	-0.879	0.043	1.369	tr|I3M435|I3M435_ICTTR	Acetyl-CoA acetyltransferase 1	ACAT1
SAVISLEGKPL	0.341	0.439	0.423	0.527	0.838	-0.255	0.439	0.357	tr|I3MY03|I3MY03_ICTTR	Cofilin, non-muscle isoform	CFL1
SESLFVSNHAY	0.007	0.030	0.015	0.050	0.664	-0.591	0.030	1.518	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SFFAVMGA	0.780	0.824	0.606	0.659	0.864	-0.211	0.659	0.181	tr|A0A287CVH5|A0A287CVH5_ICTTR	Polypyrimidine tract binding protein 2	PTBP2
SGFAAPFFIVRHQLLKK	0.096	0.168	0.200	0.276	0.632	-0.662	0.168	0.774	tr|A0A287CU43|A0A287CU43_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967835
SGFTSLLMERL	0.682	0.764	0.888	0.905	1.833	0.874	0.764	0.117	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SGPFGQIFRPDNFVFGQ	0.402	0.495	0.321	0.423	1.041	0.057	0.423	0.373	tr|I3NEP5|I3NEP5_ICTTR	Tubulin beta chain	TUBB2B
SGSAKVAFSAIRSTNH	0.058	0.116	0.074	0.146	1.557	0.639	0.116	0.936	tr|I3MWG7|I3MWG7_ICTTR	GST class-pi	GSTP1
SHLGGAVF	0.006	0.029	0.021	0.061	0.306	-1.707	0.029	1.544	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
SIGRFFG	0.037	0.088	0.139	0.222	0.805	-0.313	0.088	1.054	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGG	0.001	0.011	0.004	0.018	0.255	-1.972	0.011	1.949	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGGDRG	0.005	0.026	0.015	0.050	0.187	-2.419	0.026	1.583	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIYPAPQVS	0.335	0.437	0.200	0.276	1.791	0.840	0.276	0.559	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SLDKFLA	0.000	0.002	0.001	0.009	0.071	-3.813	0.002	2.614	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLDKFLASVSTVLTSKYR	0.076	0.147	0.139	0.222	0.332	-1.590	0.147	0.832	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLFVSNHAY	0.000	0.001	0.000	0.009	0.346	-1.532	0.001	3.169	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SLKPEFVDIINAKQ	0.016	0.048	0.021	0.061	0.611	-0.711	0.048	1.322	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
SLSAASPPMTEAGTPRRF	0.006	0.028	0.002	0.010	2.781	1.475	0.010	1.987	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SLYIANHAY	0.000	0.007	0.001	0.009	0.450	-1.152	0.007	2.176	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
SPEPEAAAAVPRRL	0.041	0.092	0.027	0.071	2.312	1.209	0.071	1.147	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SPQLEDEAKEL	0.003	0.019	0.002	0.014	2.057	1.040	0.014	1.859	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.007	0.032	0.002	0.010	2.561	1.357	0.010	1.987	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SSPETLISDLLMRESTENVPRTRLEDPSMW	0.039	0.088	0.021	0.061	2.931	1.551	0.061	1.216	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY
STLHLVLRLRGG	0.081	0.150	0.114	0.193	0.628	-0.672	0.150	0.823	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
SVLISLKQAPLVH	0.037	0.088	0.059	0.125	0.570	-0.810	0.088	1.054	tr|A0A287D1C0|A0A287D1C0_ICTTR	Clathrin light chain	CLTA
SVPRGEAAGAVQELARALAHLLEAERQE	0.006	0.028	0.008	0.033	2.190	1.131	0.028	1.555	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SVSTVLTSKYR	0.167	0.249	0.093	0.170	0.679	-0.558	0.170	0.769	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TAYAIYELAKA	0.037	0.088	0.114	0.193	0.528	-0.920	0.088	1.054	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TAYAIYELAKASFPKKQD	0.526	0.607	0.541	0.632	0.819	-0.288	0.607	0.217	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TDYLMKIL	0.117	0.190	0.093	0.170	1.417	0.503	0.170	0.769	tr|I3MNL1|I3MNL1_ICTTR	Actin beta	ACTB
TGLQGFLVFH	0.206	0.289	0.167	0.246	1.496	0.581	0.246	0.608	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TGLQGFLVFHSFGGG	0.974	0.992	0.963	0.971	1.390	0.475	0.971	0.013	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
THYKLVPHQFAH	0.003	0.022	0.000	0.009	0.383	-1.385	0.009	2.036	tr|I3MGG0|I3MGG0_ICTTR	Cytochrome c oxidase polypeptide Vb	LOC101965209
TIDFPEFL	0.011	0.039	0.008	0.033	0.573	-0.804	0.033	1.485	tr|I3MRD3|I3MRD3_ICTTR	Calmodulin	CALM1
TLHLVLRLRGG	0.011	0.039	0.008	0.033	0.368	-1.444	0.033	1.485	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
TLSKIFKLGGKDSRSGSPMARR	0.010	0.039	0.021	0.061	0.388	-1.365	0.039	1.414	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
TLYGFGG	0.002	0.019	0.002	0.014	0.396	-1.337	0.014	1.859	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TPAVHASLDKFLA	0.099	0.170	0.277	0.369	0.610	-0.713	0.170	0.770	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPAVHASLDKFLASVSTVLTSKYR	0.593	0.671	0.541	0.632	0.798	-0.325	0.632	0.200	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPEAQAAFQKVVAGVANALSHKYH	0.001	0.008	0.001	0.009	0.347	-1.525	0.008	2.086	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
TSLLMERL	0.012	0.040	0.004	0.018	0.336	-1.574	0.018	1.744	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TTMIIDHVVPEPG	0.992	0.992	0.673	0.718	1.165	0.220	0.718	0.144	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TVVYGEPITA	0.004	0.026	0.011	0.043	0.136	-2.884	0.026	1.593	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TYFPHFDL	0.011	0.039	0.059	0.125	0.518	-0.948	0.039	1.414	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYFPHFDLSHG	0.124	0.196	0.167	0.246	0.606	-0.723	0.196	0.708	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYNFAVLKLMG	0.051	0.105	0.046	0.111	0.605	-0.725	0.105	0.977	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRG	0.380	0.472	0.370	0.477	1.282	0.358	0.472	0.326	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRGTKF	0.853	0.885	1.000	1.000	0.994	-0.009	0.885	0.053	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
VGRPEWWMDYQ	0.157	0.238	0.200	0.276	1.385	0.470	0.238	0.624	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.189	0.268	0.167	0.246	1.579	0.659	0.246	0.608	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGFG	0.105	0.176	0.114	0.193	1.462	0.548	0.176	0.755	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGR	0.738	0.810	0.888	0.905	0.959	-0.060	0.810	0.092	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGRIG	0.096	0.168	0.139	0.222	1.501	0.586	0.168	0.774	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VPPVQVSPLIKL	0.117	0.190	0.093	0.170	0.649	-0.624	0.170	0.769	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
VPPVQVSPLIKLGRY	0.409	0.498	0.606	0.659	0.657	-0.607	0.498	0.303	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
YGGFLRKYP	0.000	0.004	0.001	0.009	2.783	1.477	0.004	2.442	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFLRKYPK	0.031	0.082	0.027	0.071	1.817	0.862	0.071	1.147	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFMRF	0.174	0.256	0.167	0.246	1.724	0.786	0.246	0.608	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.182	0.264	0.200	0.276	1.430	0.516	0.264	0.578	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY(-.98)	0.000	0.002	0.001	0.009	6.063	2.600	0.002	2.614	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	status	Accession	Name	GN
A(+42.01)AYKLVLIRHGE	0.003	0.020	0.001	0.009	0.456	-1.134	0.009	2.036	Down	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
AADQDLGPEAPPEGVLGA	0.010	0.038	0.011	0.043	2.401	1.264	0.038	1.415	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALL	0.001	0.011	0.002	0.010	2.761	1.465	0.010	1.987	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALLRV	0.008	0.033	0.004	0.018	2.967	1.569	0.018	1.744	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
ASWTREPLE	0.000	0.005	0.001	0.009	3.077	1.621	0.005	2.285	Up	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
EDEAAWSLDRTQQ	0.001	0.008	0.001	0.009	3.345	1.742	0.008	2.086	Up	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
KVVAGVANALSHKYH	0.011	0.039	0.008	0.033	0.386	-1.373	0.033	1.485	Down	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
LENPQPQAPARRLLPP	0.005	0.026	0.002	0.010	2.550	1.350	0.010	1.987	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
M(+42.01)DVFMKGL	0.004	0.024	0.000	0.009	0.236	-2.082	0.009	2.036	Down	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
PYQYPAL	0.001	0.011	0.002	0.010	0.246	-2.026	0.010	1.987	Down	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
Q(-17.03)EDAELQP	0.000	0.001	0.000	0.009	5.688	2.508	0.001	3.262	Up	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)EDAELQPR	0.001	0.013	0.002	0.014	3.511	1.812	0.013	1.889	Up	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
SIGRFFGG	0.001	0.011	0.004	0.018	0.255	-1.972	0.011	1.949	Down	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SLDKFLA	0.000	0.002	0.001	0.009	0.071	-3.813	0.002	2.614	Down	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLFVSNHAY	0.000	0.001	0.000	0.009	0.346	-1.532	0.001	3.169	Down	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SLSAASPPMTEAGTPRRF	0.006	0.028	0.002	0.010	2.781	1.475	0.010	1.987	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SLYIANHAY	0.000	0.007	0.001	0.009	0.450	-1.152	0.007	2.176	Down	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
SPQLEDEAKEL	0.003	0.019	0.002	0.014	2.057	1.040	0.014	1.859	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.007	0.032	0.002	0.010	2.561	1.357	0.010	1.987	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SVPRGEAAGAVQELARALAHLLEAERQE	0.006	0.028	0.008	0.033	2.190	1.131	0.028	1.555	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
THYKLVPHQFAH	0.003	0.022	0.000	0.009	0.383	-1.385	0.009	2.036	Down	tr|I3MGG0|I3MGG0_ICTTR	Cytochrome c oxidase polypeptide Vb	LOC101965209
TIDFPEFL	0.011	0.039	0.008	0.033	0.573	-0.804	0.033	1.485	Down	tr|I3MRD3|I3MRD3_ICTTR	Calmodulin	CALM1
TLHLVLRLRGG	0.011	0.039	0.008	0.033	0.368	-1.444	0.033	1.485	Down	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
TLYGFGG	0.002	0.019	0.002	0.014	0.396	-1.337	0.014	1.859	Down	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TPEAQAAFQKVVAGVANALSHKYH	0.001	0.008	0.001	0.009	0.347	-1.525	0.008	2.086	Down	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
TSLLMERL	0.012	0.040	0.004	0.018	0.336	-1.574	0.018	1.744	Down	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TVVYGEPITA	0.004	0.026	0.011	0.043	0.136	-2.884	0.026	1.593	Down	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
YGGFLRKYP	0.000	0.004	0.001	0.009	2.783	1.477	0.004	2.442	Up	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY(-.98)	0.000	0.002	0.001	0.009	6.063	2.600	0.002	2.614	Up	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

IBA vs Torpor

Full stat

Code

contrast = combo_list[[7]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: IBA over Torpor"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
A(+42.01)AYKLVLIRH	0.360	0.650	0.395	0.670	1.277	0.353	0.650	0.187	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHG	0.513	0.747	0.968	0.968	0.867	-0.206	0.747	0.127	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHGE	0.664	0.801	0.351	0.634	1.234	0.304	0.634	0.198	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)GQAFRKFLPLFDRVLVER	0.288	0.598	0.206	0.452	1.199	0.261	0.452	0.344	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
A(+42.01)LLRGVFIVAAKR	0.397	0.684	0.206	0.452	1.178	0.236	0.452	0.344	tr|I3N5Y9|I3N5Y9_ICTTR	Acetyl-CoA acyltransferase 2	ACAA2
AADQDLGPEAPPEGVLGA	0.342	0.649	0.395	0.670	0.475	-1.073	0.649	0.188	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.170	0.454	0.109	0.297	0.445	-1.168	0.297	0.528	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALL	0.012	0.075	0.001	0.022	0.411	-1.284	0.022	1.656	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALLRV	0.056	0.196	0.033	0.136	0.526	-0.928	0.136	0.867	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AEALERMFL	0.923	0.967	0.600	0.783	1.893	0.921	0.783	0.106	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
AFQKVVAGVANALSHKYH	0.665	0.801	0.545	0.782	1.224	0.292	0.782	0.107	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
AFVLVLYDELKKVI	0.410	0.695	0.492	0.745	2.247	1.168	0.695	0.158	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
ALNSVAYERNAMQNY	0.006	0.040	0.003	0.024	0.433	-1.207	0.024	1.625	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
ALNSVAYERNAMQNYE	0.003	0.036	0.007	0.040	0.347	-1.525	0.036	1.441	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
APIGLKAVVG	0.583	0.759	0.778	0.880	0.977	-0.033	0.759	0.120	tr|A0A287D563|A0A287D563_ICTTR	Syntaxin binding protein 1	STXBP1
ASWTREPLE	0.003	0.036	0.002	0.022	0.443	-1.175	0.022	1.656	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
ASWTREPLEE	0.958	0.976	0.545	0.782	1.021	0.030	0.782	0.107	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
DIDTAAKFIGAGAA	0.573	0.759	0.657	0.783	1.068	0.095	0.759	0.120	tr|I3MKX8|I3MKX8_ICTTR	ATP synthase lipid-binding protein	ATP5MC1
DILGKYVD	0.866	0.934	0.310	0.589	0.643	-0.638	0.589	0.230	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
EDEAAWSLDRTQQ	0.051	0.191	0.062	0.204	0.530	-0.916	0.191	0.719	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
EIGDEENSAKFPI(-.98)	0.246	0.562	0.272	0.545	0.677	-0.563	0.545	0.264	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
FLGEAYHHVPESQ	0.051	0.191	0.075	0.235	0.528	-0.922	0.191	0.719	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.005	0.036	0.002	0.022	0.422	-1.245	0.022	1.656	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLVFHSFGGG	0.590	0.759	0.657	0.783	1.008	0.011	0.759	0.120	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
GAAAQSLYIANHAY	0.233	0.544	0.109	0.297	1.283	0.360	0.297	0.528	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
GAEALERMFL	0.420	0.703	0.206	0.452	1.570	0.651	0.452	0.344	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
GAFVLVLYDELKKVI	0.038	0.159	0.041	0.164	0.406	-1.302	0.159	0.798	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
GASLKPEFVDIINAKQ	0.472	0.747	0.492	0.745	0.980	-0.029	0.745	0.128	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
GGFMRGL	0.212	0.517	0.051	0.189	0.367	-1.447	0.189	0.724	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GLQGFLVFH	0.213	0.517	0.177	0.423	1.416	0.502	0.423	0.374	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
KVVAGVANALSHKYH	0.491	0.747	0.657	0.783	1.299	0.378	0.747	0.127	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
LEDEAKELQ	0.205	0.517	0.310	0.589	0.573	-0.803	0.517	0.286	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
LENPQPQAPA	0.041	0.164	0.033	0.136	0.425	-1.235	0.136	0.867	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LENPQPQAPARRLLPP	0.073	0.233	0.091	0.261	0.472	-1.084	0.233	0.633	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGVLFNPYYDPLQWKSSRFE	0.002	0.036	0.003	0.024	0.522	-0.937	0.024	1.625	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LQGFLVFH	0.330	0.649	0.238	0.502	1.105	0.145	0.502	0.299	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
M(+42.01)DVFMKGL	0.660	0.801	0.545	0.782	1.064	0.089	0.782	0.107	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
MDELYPVEPEEEANGGEVL	0.001	0.032	0.002	0.022	0.304	-1.719	0.022	1.656	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MDELYPVEPEEEANGGEVLA	0.004	0.036	0.002	0.022	0.219	-2.193	0.022	1.656	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MQIFVKTL	0.534	0.753	0.778	0.880	0.694	-0.527	0.753	0.123	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLT	0.030	0.141	0.033	0.136	0.627	-0.674	0.136	0.867	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLTGK	0.574	0.759	0.272	0.545	1.017	0.025	0.545	0.264	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
PMFVVNTNVPRA	0.745	0.862	0.442	0.718	0.939	-0.091	0.718	0.144	tr|I3N9F5|I3N9F5_ICTTR	Macrophage migration inhibitory factor	MIF
PVNFKLL	0.004	0.036	0.004	0.029	2.868	1.520	0.029	1.541	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
PYQYPAL	0.028	0.141	0.009	0.051	1.943	0.959	0.051	1.293	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
Q(-17.03)EDAELQP	0.120	0.335	0.129	0.344	0.716	-0.482	0.335	0.475	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)EDAELQPR	0.003	0.036	0.003	0.024	0.337	-1.569	0.024	1.625	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)YDRVAELDQLLHY	0.001	0.032	0.002	0.022	0.491	-1.027	0.022	1.656	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPKPQQFFGLM(-.98)	0.016	0.087	0.016	0.080	0.589	-0.763	0.080	1.096	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
RTLYGFGG	0.538	0.753	0.657	0.783	0.917	-0.125	0.753	0.123	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
S(+42.01)DKPDMAEIEKFDK	0.482	0.747	0.492	0.745	0.840	-0.251	0.745	0.128	tr|A0A287CVS2|A0A287CVS2_ICTTR	Thymosin beta	Tmsb4x
S(+42.01)ILKIHAREIFD	0.510	0.747	0.968	0.968	1.144	0.193	0.747	0.127	tr|I3MIE7|I3MIE7_ICTTR	2-phospho-D-glycerate hydro-lyase	ENO1
SAMLIQKL	0.060	0.202	0.062	0.204	0.658	-0.605	0.202	0.694	tr|I3M435|I3M435_ICTTR	Acetyl-CoA acetyltransferase 1	ACAT1
SAVISLEGKPL	0.587	0.759	0.778	0.880	0.903	-0.147	0.759	0.120	tr|I3MY03|I3MY03_ICTTR	Cofilin, non-muscle isoform	CFL1
SESLFVSNHAY	0.649	0.801	0.600	0.783	1.089	0.122	0.783	0.106	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SFFAVMGA	0.901	0.961	0.968	0.968	0.772	-0.374	0.961	0.017	tr|A0A287CVH5|A0A287CVH5_ICTTR	Polypyrimidine tract binding protein 2	PTBP2
SGFAAPFFIVRHQLLKK	0.588	0.759	0.904	0.955	1.412	0.498	0.759	0.120	tr|A0A287CU43|A0A287CU43_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967835
SGFTSLLMERL	0.801	0.898	0.840	0.932	1.023	0.033	0.898	0.047	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SGPFGQIFRPDNFVFGQ	0.453	0.746	0.657	0.783	1.155	0.209	0.746	0.127	tr|I3NEP5|I3NEP5_ICTTR	Tubulin beta chain	TUBB2B
SGSAKVAFSAIRSTNH	0.013	0.075	0.005	0.035	0.419	-1.256	0.035	1.458	tr|I3MWG7|I3MWG7_ICTTR	GST class-pi	GSTP1
SHLGGAVF	0.776	0.882	0.778	0.880	1.455	0.541	0.880	0.055	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
SIGRFFG	0.278	0.588	0.272	0.545	1.395	0.480	0.545	0.264	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGG	0.119	0.335	0.075	0.235	3.578	1.839	0.235	0.630	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGGDRG	0.299	0.609	0.310	0.589	1.257	0.330	0.589	0.230	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIYPAPQVS	0.079	0.245	0.062	0.204	2.112	1.079	0.204	0.690	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SLDKFLA	0.946	0.976	0.968	0.968	0.778	-0.362	0.968	0.014	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLDKFLASVSTVLTSKYR	0.509	0.747	0.492	0.745	1.112	0.154	0.745	0.128	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLFVSNHAY	0.337	0.649	0.238	0.502	1.229	0.297	0.502	0.299	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SLKPEFVDIINAKQ	0.484	0.747	0.600	0.783	0.876	-0.190	0.747	0.127	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
SLSAASPPMTEAGTPRRF	0.036	0.159	0.007	0.040	0.402	-1.314	0.040	1.397	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SLYIANHAY	0.958	0.976	0.968	0.968	1.126	0.172	0.968	0.014	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
SPEPEAAAAVPRRL	0.056	0.196	0.062	0.204	0.562	-0.832	0.196	0.707	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SPQLEDEAKEL	0.001	0.032	0.000	0.022	0.396	-1.337	0.022	1.656	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.142	0.387	0.206	0.452	0.592	-0.756	0.387	0.412	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SSPETLISDLLMRESTENVPRTRLEDPSMW	0.275	0.588	0.177	0.423	0.452	-1.147	0.423	0.374	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY
STLHLVLRLRGG	0.515	0.747	0.442	0.718	1.113	0.154	0.718	0.144	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
SVLISLKQAPLVH	0.843	0.934	0.904	0.955	1.036	0.051	0.934	0.029	tr|A0A287D1C0|A0A287D1C0_ICTTR	Clathrin light chain	CLTA
SVPRGEAAGAVQELARALAHLLEAERQE	0.100	0.302	0.091	0.261	0.633	-0.660	0.261	0.584	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SVSTVLTSKYR	0.969	0.978	0.657	0.783	1.191	0.253	0.783	0.106	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TAYAIYELAKA	0.193	0.502	0.395	0.670	1.462	0.548	0.502	0.299	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TAYAIYELAKASFPKKQD	0.779	0.882	0.657	0.783	0.915	-0.129	0.783	0.106	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TDYLMKIL	0.369	0.656	0.152	0.395	3.063	1.615	0.395	0.403	tr|I3MNL1|I3MNL1_ICTTR	Actin beta	ACTB
TGLQGFLVFH	0.038	0.159	0.051	0.189	2.321	1.215	0.159	0.798	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TGLQGFLVFHSFGGG	0.350	0.650	0.600	0.783	1.773	0.826	0.650	0.187	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
THYKLVPHQFAH	0.687	0.818	0.840	0.932	1.163	0.218	0.818	0.087	tr|I3MGG0|I3MGG0_ICTTR	Cytochrome c oxidase polypeptide Vb	LOC101965209
TIDFPEFL	0.563	0.759	0.600	0.783	1.579	0.659	0.759	0.120	tr|I3MRD3|I3MRD3_ICTTR	Calmodulin	CALM1
TLHLVLRLRGG	0.924	0.967	0.968	0.968	1.008	0.011	0.967	0.015	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
TLSKIFKLGGKDSRSGSPMARR	0.118	0.335	0.091	0.261	0.587	-0.770	0.261	0.584	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
TLYGFGG	0.991	0.991	0.904	0.955	0.926	-0.111	0.955	0.020	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TPAVHASLDKFLA	0.868	0.934	0.778	0.880	0.836	-0.259	0.880	0.055	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPAVHASLDKFLASVSTVLTSKYR	0.357	0.650	0.351	0.634	1.444	0.530	0.634	0.198	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPEAQAAFQKVVAGVANALSHKYH	0.067	0.220	0.177	0.423	1.728	0.789	0.220	0.658	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
TSLLMERL	0.634	0.801	0.904	0.955	1.141	0.191	0.801	0.097	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TTMIIDHVVPEPG	0.857	0.934	0.657	0.783	1.252	0.324	0.783	0.106	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TVVYGEPITA	0.257	0.565	0.600	0.783	2.754	1.461	0.565	0.248	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TYFPHFDL	0.257	0.565	0.351	0.634	3.303	1.724	0.565	0.248	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYFPHFDLSHG	0.220	0.523	0.177	0.423	3.067	1.617	0.423	0.374	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYNFAVLKLMG	0.694	0.819	0.657	0.783	1.121	0.165	0.783	0.106	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRG	0.030	0.141	0.033	0.136	5.122	2.357	0.136	0.867	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRGTKF	0.655	0.801	0.545	0.782	1.235	0.304	0.782	0.107	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
VGRPEWWMDYQ	0.001	0.032	0.001	0.022	0.331	-1.597	0.022	1.656	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.026	0.139	0.033	0.136	0.632	-0.663	0.136	0.867	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGFG	0.746	0.862	0.657	0.783	1.280	0.357	0.783	0.106	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGR	0.333	0.649	0.442	0.718	1.254	0.327	0.649	0.188	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGRIG	0.387	0.677	0.904	0.955	1.101	0.138	0.677	0.169	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VPPVQVSPLIKL	0.520	0.747	0.395	0.670	1.145	0.195	0.670	0.174	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
VPPVQVSPLIKLGRY	0.004	0.036	0.004	0.029	2.337	1.224	0.029	1.541	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
YGGFLRKYP	0.001	0.032	0.001	0.022	0.423	-1.242	0.022	1.656	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFLRKYPK	0.472	0.747	0.492	0.745	0.641	-0.641	0.745	0.128	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFMRF	0.005	0.036	0.005	0.035	0.425	-1.234	0.035	1.458	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.003	0.036	0.007	0.040	0.483	-1.049	0.036	1.441	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY(-.98)	0.010	0.068	0.016	0.080	0.549	-0.864	0.068	1.170	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	status	Accession	Name	GN
ALNSVAYERNAMQNY	0.006	0.040	0.003	0.024	0.433	-1.207	0.024	1.625	Down	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
ALNSVAYERNAMQNYE	0.003	0.036	0.007	0.040	0.347	-1.525	0.036	1.441	Down	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
ASWTREPLE	0.003	0.036	0.002	0.022	0.443	-1.175	0.022	1.656	Down	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
FLGEAYHHVPESQRD	0.005	0.036	0.002	0.022	0.422	-1.245	0.022	1.656	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LGVLFNPYYDPLQWKSSRFE	0.002	0.036	0.003	0.024	0.522	-0.937	0.024	1.625	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
MDELYPVEPEEEANGGEVL	0.001	0.032	0.002	0.022	0.304	-1.719	0.022	1.656	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MDELYPVEPEEEANGGEVLA	0.004	0.036	0.002	0.022	0.219	-2.193	0.022	1.656	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
PVNFKLL	0.004	0.036	0.004	0.029	2.868	1.520	0.029	1.541	Up	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
Q(-17.03)EDAELQPR	0.003	0.036	0.003	0.024	0.337	-1.569	0.024	1.625	Down	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)YDRVAELDQLLHY	0.001	0.032	0.002	0.022	0.491	-1.027	0.022	1.656	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
SPQLEDEAKEL	0.001	0.032	0.000	0.022	0.396	-1.337	0.022	1.656	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VGRPEWWMDYQ	0.001	0.032	0.001	0.022	0.331	-1.597	0.022	1.656	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VPPVQVSPLIKLGRY	0.004	0.036	0.004	0.029	2.337	1.224	0.029	1.541	Up	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
YGGFLRKYP	0.001	0.032	0.001	0.022	0.423	-1.242	0.022	1.656	Down	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFMRF	0.005	0.036	0.005	0.035	0.425	-1.234	0.035	1.458	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.003	0.036	0.007	0.040	0.483	-1.049	0.036	1.441	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

March vs October

Full stat

Code

contrast = combo_list[[8]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: March over October"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
A(+42.01)AYKLVLIRH	0.117	0.145	0.167	0.199	0.424	-1.237	0.145	0.838	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHG	0.000	0.002	0.002	0.004	0.440	-1.184	0.002	2.734	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHGE	0.000	0.001	0.000	0.001	0.353	-1.504	0.001	3.266	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)GQAFRKFLPLFDRVLVER	0.004	0.008	0.008	0.014	0.384	-1.381	0.008	2.083	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
A(+42.01)LLRGVFIVAAKR	0.001	0.002	0.002	0.004	0.217	-2.207	0.002	2.670	tr|I3N5Y9|I3N5Y9_ICTTR	Acetyl-CoA acyltransferase 2	ACAA2
AADQDLGPEAPPEGVLGA	0.000	0.001	0.000	0.001	5.924	2.567	0.001	3.266	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.001	0.002	0.000	0.001	2.668	1.416	0.001	2.925	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALL	0.000	0.001	0.000	0.001	11.138	3.477	0.001	3.266	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALLRV	0.004	0.008	0.000	0.001	6.952	2.797	0.001	2.925	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AEALERMFL	0.005	0.010	0.011	0.019	0.229	-2.129	0.010	1.997	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
AFQKVVAGVANALSHKYH	0.015	0.024	0.015	0.024	0.373	-1.424	0.024	1.614	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
AFVLVLYDELKKVI	0.578	0.616	0.236	0.275	0.692	-0.531	0.275	0.560	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
ALNSVAYERNAMQNY	0.081	0.107	0.074	0.098	1.972	0.979	0.098	1.008	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
ALNSVAYERNAMQNYE	0.000	0.001	0.000	0.001	7.654	2.936	0.001	3.291	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
APIGLKAVVG	0.188	0.224	0.423	0.470	0.772	-0.374	0.224	0.651	tr|A0A287D563|A0A287D563_ICTTR	Syntaxin binding protein 1	STXBP1
ASWTREPLE	0.001	0.003	0.000	0.001	4.987	2.318	0.001	2.925	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
ASWTREPLEE	0.008	0.014	0.004	0.007	2.637	1.399	0.007	2.153	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
DIDTAAKFIGAGAA	0.490	0.538	0.673	0.698	1.081	0.112	0.538	0.269	tr|I3MKX8|I3MKX8_ICTTR	ATP synthase lipid-binding protein	ATP5MC1
DILGKYVD	0.002	0.006	0.004	0.007	0.376	-1.410	0.006	2.259	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
EDEAAWSLDRTQQ	0.001	0.002	0.000	0.001	6.332	2.663	0.001	3.036	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
EIGDEENSAKFPI(-.98)	0.018	0.028	0.021	0.032	2.393	1.259	0.028	1.550	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
FLGEAYHHVPESQ	0.023	0.035	0.015	0.024	3.531	1.820	0.024	1.613	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.003	0.006	0.000	0.001	5.814	2.539	0.001	2.925	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLVFHSFGGG	0.090	0.116	0.167	0.199	0.614	-0.704	0.116	0.936	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
GAAAQSLYIANHAY	0.070	0.093	0.114	0.145	0.302	-1.727	0.093	1.030	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
GAEALERMFL	0.004	0.008	0.008	0.014	0.280	-1.835	0.008	2.120	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
GAFVLVLYDELKKVI	0.848	0.856	0.888	0.888	0.814	-0.297	0.856	0.068	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
GASLKPEFVDIINAKQ	0.778	0.800	0.888	0.888	0.958	-0.062	0.800	0.097	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
GGFMRGL	0.867	0.867	0.673	0.698	1.865	0.899	0.698	0.156	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GLQGFLVFH	0.001	0.003	0.002	0.006	0.247	-2.015	0.003	2.510	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
KVVAGVANALSHKYH	0.067	0.090	0.059	0.083	0.237	-2.080	0.083	1.081	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
LEDEAKELQ	0.639	0.669	0.606	0.646	0.778	-0.363	0.646	0.190	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
LENPQPQAPA	0.000	0.001	0.000	0.001	6.312	2.658	0.001	3.291	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LENPQPQAPARRLLPP	0.001	0.003	0.000	0.001	3.191	1.674	0.001	2.925	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGVLFNPYYDPLQWKSSRFE	0.000	0.001	0.000	0.001	3.923	1.972	0.001	3.044	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LQGFLVFH	0.000	0.001	0.000	0.001	0.124	-3.007	0.001	3.266	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
M(+42.01)DVFMKGL	0.000	0.002	0.000	0.001	0.118	-3.077	0.001	3.266	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
MDELYPVEPEEEANGGEVL	0.008	0.014	0.000	0.001	5.282	2.401	0.001	3.266	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MDELYPVEPEEEANGGEVLA	0.000	0.001	0.000	0.001	5.876	2.555	0.001	2.925	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MQIFVKTL	0.031	0.046	0.074	0.098	0.433	-1.208	0.046	1.340	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLT	0.263	0.307	0.481	0.528	0.763	-0.390	0.307	0.513	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLTGK	0.534	0.581	0.541	0.589	0.759	-0.399	0.581	0.236	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
PMFVVNTNVPRA	0.048	0.069	0.027	0.041	0.607	-0.720	0.041	1.388	tr|I3N9F5|I3N9F5_ICTTR	Macrophage migration inhibitory factor	MIF
PVNFKLL	0.001	0.003	0.004	0.007	0.183	-2.447	0.003	2.569	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
PYQYPAL	0.000	0.000	0.000	0.001	0.075	-3.730	0.000	4.957	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
Q(-17.03)EDAELQP	0.000	0.000	0.000	0.001	27.812	4.798	0.000	6.928	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)EDAELQPR	0.001	0.003	0.001	0.003	5.759	2.526	0.003	2.547	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)YDRVAELDQLLHY	0.000	0.001	0.000	0.001	3.313	1.728	0.001	3.266	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPKPQQFFGLM(-.98)	0.567	0.610	0.815	0.830	1.253	0.325	0.610	0.215	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
RTLYGFGG	0.036	0.053	0.074	0.098	0.598	-0.741	0.053	1.273	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
S(+42.01)DKPDMAEIEKFDK	0.598	0.632	0.606	0.646	1.048	0.068	0.632	0.199	tr|A0A287CVS2|A0A287CVS2_ICTTR	Thymosin beta	Tmsb4x
S(+42.01)ILKIHAREIFD	0.000	0.001	0.002	0.006	0.263	-1.928	0.001	2.978	tr|I3MIE7|I3MIE7_ICTTR	2-phospho-D-glycerate hydro-lyase	ENO1
SAMLIQKL	0.042	0.061	0.027	0.041	0.390	-1.357	0.041	1.388	tr|I3M435|I3M435_ICTTR	Acetyl-CoA acetyltransferase 1	ACAT1
SAVISLEGKPL	0.051	0.071	0.015	0.024	0.545	-0.876	0.024	1.613	tr|I3MY03|I3MY03_ICTTR	Cofilin, non-muscle isoform	CFL1
SESLFVSNHAY	0.000	0.002	0.002	0.004	0.488	-1.035	0.002	2.732	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SFFAVMGA	0.375	0.424	0.423	0.470	0.878	-0.188	0.424	0.373	tr|A0A287CVH5|A0A287CVH5_ICTTR	Polypyrimidine tract binding protein 2	PTBP2
SGFAAPFFIVRHQLLKK	0.002	0.006	0.004	0.007	0.215	-2.217	0.006	2.259	tr|A0A287CU43|A0A287CU43_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967835
SGFTSLLMERL	0.246	0.290	0.139	0.171	0.755	-0.405	0.171	0.767	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SGPFGQIFRPDNFVFGQ	0.388	0.434	0.277	0.319	0.755	-0.406	0.319	0.496	tr|I3NEP5|I3NEP5_ICTTR	Tubulin beta chain	TUBB2B
SGSAKVAFSAIRSTNH	0.025	0.038	0.006	0.010	2.522	1.335	0.010	2.002	tr|I3MWG7|I3MWG7_ICTTR	GST class-pi	GSTP1
SHLGGAVF	0.000	0.002	0.001	0.002	0.140	-2.836	0.002	2.747	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
SIGRFFG	0.001	0.004	0.004	0.007	0.201	-2.313	0.004	2.451	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGG	0.000	0.001	0.001	0.002	0.063	-3.997	0.001	3.109	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGGDRG	0.000	0.001	0.000	0.001	0.167	-2.578	0.001	3.036	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIYPAPQVS	0.052	0.071	0.114	0.145	0.788	-0.344	0.071	1.147	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SLDKFLA	0.000	0.000	0.000	0.001	0.037	-4.763	0.000	4.242	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLDKFLASVSTVLTSKYR	0.011	0.018	0.027	0.041	0.269	-1.893	0.018	1.735	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLFVSNHAY	0.000	0.000	0.000	0.001	0.185	-2.436	0.000	6.255	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SLKPEFVDIINAKQ	0.096	0.122	0.046	0.066	0.470	-1.090	0.066	1.182	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
SLSAASPPMTEAGTPRRF	0.000	0.001	0.001	0.003	3.444	1.784	0.001	2.902	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SLYIANHAY	0.000	0.001	0.000	0.001	0.284	-1.816	0.001	3.044	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
SPEPEAAAAVPRRL	0.451	0.501	0.423	0.470	1.307	0.386	0.470	0.328	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SPQLEDEAKEL	0.010	0.016	0.000	0.001	3.658	1.871	0.001	2.925	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.001	0.003	0.000	0.001	5.694	2.510	0.001	2.925	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SSPETLISDLLMRESTENVPRTRLEDPSMW	0.003	0.006	0.001	0.003	4.488	2.166	0.003	2.547	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY
STLHLVLRLRGG	0.141	0.171	0.139	0.171	0.739	-0.437	0.171	0.767	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
SVLISLKQAPLVH	0.002	0.006	0.002	0.006	0.385	-1.378	0.006	2.259	tr|A0A287D1C0|A0A287D1C0_ICTTR	Clathrin light chain	CLTA
SVPRGEAAGAVQELARALAHLLEAERQE	0.003	0.006	0.001	0.002	3.374	1.754	0.002	2.747	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SVSTVLTSKYR	0.139	0.170	0.046	0.066	0.226	-2.145	0.066	1.182	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TAYAIYELAKA	0.006	0.011	0.011	0.019	0.282	-1.826	0.011	1.952	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TAYAIYELAKASFPKKQD	0.085	0.111	0.074	0.098	0.578	-0.790	0.098	1.008	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TDYLMKIL	0.005	0.009	0.036	0.052	0.389	-1.363	0.009	2.025	tr|I3MNL1|I3MNL1_ICTTR	Actin beta	ACTB
TGLQGFLVFH	0.007	0.013	0.006	0.010	0.351	-1.509	0.010	2.002	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TGLQGFLVFHSFGGG	0.802	0.816	0.673	0.698	1.233	0.303	0.698	0.156	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
THYKLVPHQFAH	0.009	0.015	0.011	0.019	0.333	-1.588	0.015	1.833	tr|I3MGG0|I3MGG0_ICTTR	Cytochrome c oxidase polypeptide Vb	LOC101965209
TIDFPEFL	0.002	0.004	0.004	0.007	0.229	-2.126	0.004	2.387	tr|I3MRD3|I3MRD3_ICTTR	Calmodulin	CALM1
TLHLVLRLRGG	0.067	0.090	0.074	0.098	0.639	-0.646	0.090	1.044	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
TLSKIFKLGGKDSRSGSPMARR	0.001	0.004	0.004	0.007	0.270	-1.892	0.004	2.439	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
TLYGFGG	0.000	0.002	0.001	0.002	0.303	-1.722	0.002	2.747	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TPAVHASLDKFLA	0.030	0.046	0.036	0.052	0.378	-1.402	0.046	1.340	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPAVHASLDKFLASVSTVLTSKYR	0.179	0.216	0.139	0.171	0.494	-1.017	0.171	0.767	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPEAQAAFQKVVAGVANALSHKYH	0.000	0.001	0.000	0.001	0.169	-2.569	0.001	3.266	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
TSLLMERL	0.001	0.002	0.002	0.004	0.084	-3.575	0.002	2.682	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TTMIIDHVVPEPG	0.112	0.141	0.167	0.199	0.521	-0.941	0.141	0.850	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TVVYGEPITA	0.000	0.000	0.000	0.001	0.042	-4.577	0.000	5.000	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TYFPHFDL	0.002	0.006	0.004	0.007	0.245	-2.028	0.006	2.259	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYFPHFDLSHG	0.001	0.004	0.001	0.002	0.195	-2.356	0.002	2.747	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYNFAVLKLMG	0.003	0.006	0.004	0.007	0.239	-2.067	0.006	2.206	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRG	0.001	0.003	0.002	0.004	0.126	-2.991	0.003	2.478	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRGTKF	0.039	0.057	0.093	0.121	0.357	-1.487	0.057	1.248	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
VGRPEWWMDYQ	0.000	0.001	0.000	0.001	4.828	2.271	0.001	3.266	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.003	0.006	0.006	0.010	2.814	1.492	0.006	2.194	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGFG	0.347	0.397	0.200	0.235	0.483	-1.048	0.235	0.628	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGR	0.277	0.320	0.423	0.470	0.862	-0.214	0.320	0.494	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGRIG	0.758	0.786	0.743	0.763	0.898	-0.155	0.763	0.117	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VPPVQVSPLIKL	0.018	0.028	0.021	0.032	0.561	-0.835	0.028	1.552	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
VPPVQVSPLIKLGRY	0.002	0.005	0.002	0.004	0.300	-1.737	0.004	2.420	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
YGGFLRKYP	0.000	0.002	0.000	0.001	9.327	3.221	0.001	3.266	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFLRKYPK	0.013	0.021	0.002	0.004	2.807	1.489	0.004	2.420	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFMRF	0.002	0.005	0.002	0.006	3.829	1.937	0.005	2.338	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.000	0.001	0.000	0.001	3.598	1.847	0.001	2.925	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY(-.98)	0.000	0.001	0.000	0.001	6.494	2.699	0.001	3.044	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	status	Accession	Name	GN
A(+42.01)AYKLVLIRHG	0.000	0.002	0.002	0.004	0.440	-1.184	0.002	2.734	Down	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHGE	0.000	0.001	0.000	0.001	0.353	-1.504	0.001	3.266	Down	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)GQAFRKFLPLFDRVLVER	0.004	0.008	0.008	0.014	0.384	-1.381	0.008	2.083	Down	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
A(+42.01)LLRGVFIVAAKR	0.001	0.002	0.002	0.004	0.217	-2.207	0.002	2.670	Down	tr|I3N5Y9|I3N5Y9_ICTTR	Acetyl-CoA acyltransferase 2	ACAA2
AADQDLGPEAPPEGVLGA	0.000	0.001	0.000	0.001	5.924	2.567	0.001	3.266	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.001	0.002	0.000	0.001	2.668	1.416	0.001	2.925	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALL	0.000	0.001	0.000	0.001	11.138	3.477	0.001	3.266	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALLRV	0.004	0.008	0.000	0.001	6.952	2.797	0.001	2.925	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AEALERMFL	0.005	0.010	0.011	0.019	0.229	-2.129	0.010	1.997	Down	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
AFQKVVAGVANALSHKYH	0.015	0.024	0.015	0.024	0.373	-1.424	0.024	1.614	Down	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
ALNSVAYERNAMQNYE	0.000	0.001	0.000	0.001	7.654	2.936	0.001	3.291	Up	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
ASWTREPLE	0.001	0.003	0.000	0.001	4.987	2.318	0.001	2.925	Up	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
ASWTREPLEE	0.008	0.014	0.004	0.007	2.637	1.399	0.007	2.153	Up	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
DILGKYVD	0.002	0.006	0.004	0.007	0.376	-1.410	0.006	2.259	Down	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
EDEAAWSLDRTQQ	0.001	0.002	0.000	0.001	6.332	2.663	0.001	3.036	Up	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
EIGDEENSAKFPI(-.98)	0.018	0.028	0.021	0.032	2.393	1.259	0.028	1.550	Up	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
FLGEAYHHVPESQ	0.023	0.035	0.015	0.024	3.531	1.820	0.024	1.613	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.003	0.006	0.000	0.001	5.814	2.539	0.001	2.925	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GAEALERMFL	0.004	0.008	0.008	0.014	0.280	-1.835	0.008	2.120	Down	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
GLQGFLVFH	0.001	0.003	0.002	0.006	0.247	-2.015	0.003	2.510	Down	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
LENPQPQAPA	0.000	0.001	0.000	0.001	6.312	2.658	0.001	3.291	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LENPQPQAPARRLLPP	0.001	0.003	0.000	0.001	3.191	1.674	0.001	2.925	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGVLFNPYYDPLQWKSSRFE	0.000	0.001	0.000	0.001	3.923	1.972	0.001	3.044	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LQGFLVFH	0.000	0.001	0.000	0.001	0.124	-3.007	0.001	3.266	Down	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
M(+42.01)DVFMKGL	0.000	0.002	0.000	0.001	0.118	-3.077	0.001	3.266	Down	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
MDELYPVEPEEEANGGEVL	0.008	0.014	0.000	0.001	5.282	2.401	0.001	3.266	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MDELYPVEPEEEANGGEVLA	0.000	0.001	0.000	0.001	5.876	2.555	0.001	2.925	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
PVNFKLL	0.001	0.003	0.004	0.007	0.183	-2.447	0.003	2.569	Down	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
PYQYPAL	0.000	0.000	0.000	0.001	0.075	-3.730	0.000	4.957	Down	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
Q(-17.03)EDAELQP	0.000	0.000	0.000	0.001	27.812	4.798	0.000	6.928	Up	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)EDAELQPR	0.001	0.003	0.001	0.003	5.759	2.526	0.003	2.547	Up	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)YDRVAELDQLLHY	0.000	0.001	0.000	0.001	3.313	1.728	0.001	3.266	Up	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
S(+42.01)ILKIHAREIFD	0.000	0.001	0.002	0.006	0.263	-1.928	0.001	2.978	Down	tr|I3MIE7|I3MIE7_ICTTR	2-phospho-D-glycerate hydro-lyase	ENO1
SESLFVSNHAY	0.000	0.002	0.002	0.004	0.488	-1.035	0.002	2.732	Down	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SGFAAPFFIVRHQLLKK	0.002	0.006	0.004	0.007	0.215	-2.217	0.006	2.259	Down	tr|A0A287CU43|A0A287CU43_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967835
SGSAKVAFSAIRSTNH	0.025	0.038	0.006	0.010	2.522	1.335	0.010	2.002	Up	tr|I3MWG7|I3MWG7_ICTTR	GST class-pi	GSTP1
SHLGGAVF	0.000	0.002	0.001	0.002	0.140	-2.836	0.002	2.747	Down	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
SIGRFFG	0.001	0.004	0.004	0.007	0.201	-2.313	0.004	2.451	Down	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGG	0.000	0.001	0.001	0.002	0.063	-3.997	0.001	3.109	Down	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGGDRG	0.000	0.001	0.000	0.001	0.167	-2.578	0.001	3.036	Down	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SLDKFLA	0.000	0.000	0.000	0.001	0.037	-4.763	0.000	4.242	Down	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLDKFLASVSTVLTSKYR	0.011	0.018	0.027	0.041	0.269	-1.893	0.018	1.735	Down	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLFVSNHAY	0.000	0.000	0.000	0.001	0.185	-2.436	0.000	6.255	Down	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SLSAASPPMTEAGTPRRF	0.000	0.001	0.001	0.003	3.444	1.784	0.001	2.902	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SLYIANHAY	0.000	0.001	0.000	0.001	0.284	-1.816	0.001	3.044	Down	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
SPQLEDEAKEL	0.010	0.016	0.000	0.001	3.658	1.871	0.001	2.925	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.001	0.003	0.000	0.001	5.694	2.510	0.001	2.925	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SSPETLISDLLMRESTENVPRTRLEDPSMW	0.003	0.006	0.001	0.003	4.488	2.166	0.003	2.547	Up	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY
SVLISLKQAPLVH	0.002	0.006	0.002	0.006	0.385	-1.378	0.006	2.259	Down	tr|A0A287D1C0|A0A287D1C0_ICTTR	Clathrin light chain	CLTA
SVPRGEAAGAVQELARALAHLLEAERQE	0.003	0.006	0.001	0.002	3.374	1.754	0.002	2.747	Up	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
TAYAIYELAKA	0.006	0.011	0.011	0.019	0.282	-1.826	0.011	1.952	Down	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TGLQGFLVFH	0.007	0.013	0.006	0.010	0.351	-1.509	0.010	2.002	Down	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
THYKLVPHQFAH	0.009	0.015	0.011	0.019	0.333	-1.588	0.015	1.833	Down	tr|I3MGG0|I3MGG0_ICTTR	Cytochrome c oxidase polypeptide Vb	LOC101965209
TIDFPEFL	0.002	0.004	0.004	0.007	0.229	-2.126	0.004	2.387	Down	tr|I3MRD3|I3MRD3_ICTTR	Calmodulin	CALM1
TLSKIFKLGGKDSRSGSPMARR	0.001	0.004	0.004	0.007	0.270	-1.892	0.004	2.439	Down	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
TLYGFGG	0.000	0.002	0.001	0.002	0.303	-1.722	0.002	2.747	Down	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TPEAQAAFQKVVAGVANALSHKYH	0.000	0.001	0.000	0.001	0.169	-2.569	0.001	3.266	Down	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
TSLLMERL	0.001	0.002	0.002	0.004	0.084	-3.575	0.002	2.682	Down	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TVVYGEPITA	0.000	0.000	0.000	0.001	0.042	-4.577	0.000	5.000	Down	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TYFPHFDL	0.002	0.006	0.004	0.007	0.245	-2.028	0.006	2.259	Down	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYFPHFDLSHG	0.001	0.004	0.001	0.002	0.195	-2.356	0.002	2.747	Down	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYNFAVLKLMG	0.003	0.006	0.004	0.007	0.239	-2.067	0.006	2.206	Down	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRG	0.001	0.003	0.002	0.004	0.126	-2.991	0.003	2.478	Down	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
VGRPEWWMDYQ	0.000	0.001	0.000	0.001	4.828	2.271	0.001	3.266	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.003	0.006	0.006	0.010	2.814	1.492	0.006	2.194	Up	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VPPVQVSPLIKL	0.018	0.028	0.021	0.032	0.561	-0.835	0.028	1.552	Down	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
VPPVQVSPLIKLGRY	0.002	0.005	0.002	0.004	0.300	-1.737	0.004	2.420	Down	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
YGGFLRKYP	0.000	0.002	0.000	0.001	9.327	3.221	0.001	3.266	Up	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFLRKYPK	0.013	0.021	0.002	0.004	2.807	1.489	0.004	2.420	Up	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFMRF	0.002	0.005	0.002	0.006	3.829	1.937	0.005	2.338	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.000	0.001	0.000	0.001	3.598	1.847	0.001	2.925	Up	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY(-.98)	0.000	0.001	0.000	0.001	6.494	2.699	0.001	3.044	Up	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

March vs Torpor

Full stat

Code

contrast = combo_list[[9]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: March over Torpor"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
A(+42.01)AYKLVLIRH	0.382	0.679	0.177	0.423	0.595	-0.748	0.423	0.374	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHG	0.018	0.167	0.033	0.183	0.621	-0.686	0.167	0.778	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHGE	0.406	0.700	0.657	0.877	0.956	-0.065	0.700	0.155	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)GQAFRKFLPLFDRVLVER	0.839	0.921	0.968	0.977	0.949	-0.076	0.921	0.036	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
A(+42.01)LLRGVFIVAAKR	0.006	0.104	0.007	0.097	0.539	-0.893	0.097	1.015	tr|I3N5Y9|I3N5Y9_ICTTR	Acetyl-CoA acyltransferase 2	ACAA2
AADQDLGPEAPPEGVLGA	0.320	0.608	0.310	0.543	1.173	0.230	0.543	0.266	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.166	0.414	0.152	0.405	0.807	-0.309	0.405	0.393	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALL	0.400	0.700	0.238	0.467	1.657	0.728	0.467	0.331	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALLRV	0.449	0.708	0.840	0.923	1.231	0.300	0.708	0.150	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AEALERMFL	0.154	0.394	0.129	0.380	0.820	-0.287	0.380	0.421	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
AFQKVVAGVANALSHKYH	0.025	0.189	0.020	0.142	0.469	-1.092	0.142	0.846	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
AFVLVLYDELKKVI	0.561	0.766	0.177	0.423	1.101	0.139	0.423	0.374	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
ALNSVAYERNAMQNY	0.910	0.953	0.717	0.882	0.710	-0.493	0.882	0.054	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
ALNSVAYERNAMQNYE	0.577	0.766	0.351	0.578	1.547	0.629	0.578	0.238	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
APIGLKAVVG	0.078	0.336	0.152	0.405	0.700	-0.515	0.336	0.473	tr|A0A287D563|A0A287D563_ICTTR	Syntaxin binding protein 1	STXBP1
ASWTREPLE	0.816	0.905	0.840	0.923	0.718	-0.478	0.905	0.044	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
ASWTREPLEE	0.890	0.942	0.717	0.882	1.221	0.288	0.882	0.054	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
DIDTAAKFIGAGAA	0.179	0.426	0.177	0.423	0.570	-0.810	0.423	0.374	tr|I3MKX8|I3MKX8_ICTTR	ATP synthase lipid-binding protein	ATP5MC1
DILGKYVD	0.318	0.608	0.442	0.660	0.799	-0.324	0.608	0.216	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
EDEAAWSLDRTQQ	0.355	0.651	0.492	0.716	1.003	0.005	0.651	0.186	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
EIGDEENSAKFPI(-.98)	0.892	0.942	0.657	0.877	0.821	-0.285	0.877	0.057	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
FLGEAYHHVPESQ	0.488	0.729	0.904	0.964	1.128	0.173	0.729	0.137	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.084	0.336	0.091	0.328	1.644	0.717	0.328	0.484	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLVFHSFGGG	0.153	0.394	0.272	0.492	0.792	-0.336	0.394	0.404	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
GAAAQSLYIANHAY	0.302	0.594	0.206	0.444	0.450	-1.153	0.444	0.353	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
GAEALERMFL	0.038	0.207	0.033	0.183	0.497	-1.008	0.183	0.736	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
GAFVLVLYDELKKVI	0.090	0.336	0.129	0.380	0.377	-1.406	0.336	0.473	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
GASLKPEFVDIINAKQ	0.867	0.934	0.778	0.908	1.107	0.147	0.908	0.042	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
GGFMRGL	0.687	0.819	0.778	0.908	0.720	-0.473	0.819	0.087	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GLQGFLVFH	0.004	0.104	0.005	0.097	0.468	-1.095	0.097	1.015	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
KVVAGVANALSHKYH	0.654	0.812	0.840	0.923	0.796	-0.329	0.812	0.090	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
LEDEAKELQ	0.277	0.554	0.272	0.492	1.284	0.360	0.492	0.308	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
LENPQPQAPA	0.425	0.700	0.395	0.615	1.266	0.341	0.615	0.211	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LENPQPQAPARRLLPP	0.183	0.428	0.238	0.467	0.590	-0.760	0.428	0.368	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGVLFNPYYDPLQWKSSRFE	0.047	0.240	0.062	0.257	1.693	0.760	0.240	0.619	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LQGFLVFH	0.001	0.055	0.007	0.097	0.449	-1.155	0.055	1.261	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
M(+42.01)DVFMKGL	0.010	0.121	0.012	0.097	0.534	-0.906	0.097	1.015	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
MDELYPVEPEEEANGGEVL	0.647	0.812	0.600	0.840	0.763	-0.391	0.812	0.090	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MDELYPVEPEEEANGGEVLA	0.464	0.708	0.840	0.923	0.897	-0.157	0.708	0.150	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MQIFVKTL	0.663	0.812	0.904	0.964	0.822	-0.282	0.812	0.090	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLT	0.351	0.651	0.395	0.615	0.839	-0.254	0.615	0.211	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLTGK	0.458	0.708	0.351	0.578	0.842	-0.248	0.578	0.238	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
PMFVVNTNVPRA	0.027	0.191	0.012	0.097	0.499	-1.004	0.097	1.015	tr|I3N9F5|I3N9F5_ICTTR	Macrophage migration inhibitory factor	MIF
PVNFKLL	0.666	0.812	0.717	0.882	0.907	-0.141	0.812	0.090	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
PYQYPAL	0.011	0.122	0.020	0.142	0.596	-0.746	0.122	0.914	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
Q(-17.03)EDAELQP	0.008	0.121	0.007	0.097	3.501	1.808	0.097	1.015	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)EDAELQPR	0.750	0.857	0.968	0.977	0.553	-0.855	0.857	0.067	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)YDRVAELDQLLHY	0.468	0.708	0.395	0.615	1.193	0.255	0.615	0.211	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPKPQQFFGLM(-.98)	0.375	0.677	0.351	0.578	0.733	-0.447	0.578	0.238	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
RTLYGFGG	0.033	0.204	0.051	0.227	0.607	-0.719	0.204	0.690	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
S(+42.01)DKPDMAEIEKFDK	0.581	0.766	0.600	0.840	1.040	0.057	0.766	0.116	tr|A0A287CVS2|A0A287CVS2_ICTTR	Thymosin beta	Tmsb4x
S(+42.01)ILKIHAREIFD	0.033	0.204	0.026	0.171	0.559	-0.839	0.171	0.767	tr|I3MIE7|I3MIE7_ICTTR	2-phospho-D-glycerate hydro-lyase	ENO1
SAMLIQKL	0.088	0.336	0.033	0.183	0.472	-1.083	0.183	0.736	tr|I3M435|I3M435_ICTTR	Acetyl-CoA acetyltransferase 1	ACAT1
SAVISLEGKPL	0.082	0.336	0.012	0.097	0.587	-0.769	0.097	1.015	tr|I3MY03|I3MY03_ICTTR	Cofilin, non-muscle isoform	CFL1
SESLFVSNHAY	0.179	0.426	0.091	0.328	0.800	-0.322	0.328	0.484	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SFFAVMGA	0.570	0.766	0.778	0.908	0.784	-0.350	0.766	0.116	tr|A0A287CVH5|A0A287CVH5_ICTTR	Polypyrimidine tract binding protein 2	PTBP2
SGFAAPFFIVRHQLLKK	0.038	0.207	0.051	0.227	0.481	-1.057	0.207	0.684	tr|A0A287CU43|A0A287CU43_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967835
SGFTSLLMERL	0.140	0.394	0.051	0.227	0.422	-1.246	0.227	0.644	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SGPFGQIFRPDNFVFGQ	0.432	0.701	0.545	0.782	0.838	-0.254	0.701	0.154	tr|I3NEP5|I3NEP5_ICTTR	Tubulin beta chain	TUBB2B
SGSAKVAFSAIRSTNH	0.674	0.812	0.717	0.882	0.678	-0.561	0.812	0.090	tr|I3MWG7|I3MWG7_ICTTR	GST class-pi	GSTP1
SHLGGAVF	0.216	0.474	0.272	0.492	0.665	-0.588	0.474	0.324	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
SIGRFFG	0.001	0.055	0.002	0.097	0.349	-1.520	0.055	1.261	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGG	0.228	0.492	0.177	0.423	0.879	-0.186	0.423	0.374	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGGDRG	0.861	0.934	0.840	0.923	1.126	0.171	0.923	0.035	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIYPAPQVS	0.577	0.766	0.442	0.660	0.930	-0.105	0.660	0.180	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SLDKFLA	0.001	0.055	0.002	0.097	0.403	-1.311	0.055	1.261	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLDKFLASVSTVLTSKYR	0.928	0.962	0.778	0.908	0.901	-0.150	0.908	0.042	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLFVSNHAY	0.013	0.131	0.012	0.097	0.657	-0.607	0.097	1.015	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SLKPEFVDIINAKQ	0.500	0.736	0.177	0.423	0.674	-0.569	0.423	0.374	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
SLSAASPPMTEAGTPRRF	0.021	0.175	0.012	0.097	0.498	-1.005	0.097	1.015	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SLYIANHAY	0.141	0.394	0.152	0.405	0.711	-0.492	0.394	0.404	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
SPEPEAAAAVPRRL	0.009	0.121	0.009	0.097	0.318	-1.655	0.097	1.015	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SPQLEDEAKEL	0.795	0.900	0.657	0.877	0.704	-0.507	0.877	0.057	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.743	0.857	0.492	0.716	1.317	0.397	0.716	0.145	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SSPETLISDLLMRESTENVPRTRLEDPSMW	0.089	0.336	0.238	0.467	0.692	-0.532	0.336	0.473	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY
STLHLVLRLRGG	0.202	0.461	0.206	0.444	1.310	0.389	0.444	0.353	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
SVLISLKQAPLVH	0.095	0.341	0.129	0.380	0.699	-0.516	0.341	0.467	tr|A0A287D1C0|A0A287D1C0_ICTTR	Clathrin light chain	CLTA
SVPRGEAAGAVQELARALAHLLEAERQE	0.673	0.812	0.968	0.977	0.975	-0.036	0.812	0.090	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SVSTVLTSKYR	0.423	0.700	0.272	0.492	0.397	-1.334	0.492	0.308	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TAYAIYELAKA	0.511	0.743	0.351	0.578	0.780	-0.358	0.578	0.238	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TAYAIYELAKASFPKKQD	0.155	0.394	0.075	0.291	0.646	-0.630	0.291	0.536	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TDYLMKIL	0.121	0.375	0.206	0.444	0.840	-0.251	0.375	0.426	tr|I3MNL1|I3MNL1_ICTTR	Actin beta	ACTB
TGLQGFLVFH	0.154	0.394	0.109	0.369	0.545	-0.875	0.369	0.433	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TGLQGFLVFHSFGGG	0.536	0.766	0.968	0.977	1.573	0.654	0.766	0.116	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
THYKLVPHQFAH	0.730	0.851	0.840	0.923	1.010	0.014	0.851	0.070	tr|I3MGG0|I3MGG0_ICTTR	Cytochrome c oxidase polypeptide Vb	LOC101965209
TIDFPEFL	0.273	0.554	0.310	0.543	0.632	-0.662	0.543	0.266	tr|I3MRD3|I3MRD3_ICTTR	Calmodulin	CALM1
TLHLVLRLRGG	0.264	0.550	0.152	0.405	1.752	0.809	0.405	0.393	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
TLSKIFKLGGKDSRSGSPMARR	0.005	0.104	0.004	0.097	0.407	-1.297	0.097	1.015	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
TLYGFGG	0.265	0.550	0.395	0.615	0.709	-0.496	0.550	0.259	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TPAVHASLDKFLA	0.209	0.469	0.062	0.257	0.518	-0.949	0.257	0.590	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPAVHASLDKFLASVSTVLTSKYR	0.947	0.973	0.968	0.977	0.894	-0.162	0.973	0.012	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPEAQAAFQKVVAGVANALSHKYH	0.582	0.766	0.717	0.882	0.838	-0.255	0.766	0.116	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
TSLLMERL	0.022	0.175	0.012	0.097	0.285	-1.810	0.097	1.015	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TTMIIDHVVPEPG	0.151	0.394	0.206	0.444	0.560	-0.837	0.394	0.404	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TVVYGEPITA	0.070	0.336	0.051	0.227	0.852	-0.232	0.227	0.644	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TYFPHFDL	0.451	0.708	0.238	0.467	1.562	0.643	0.467	0.331	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYFPHFDLSHG	0.124	0.375	0.075	0.291	0.989	-0.017	0.291	0.536	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYNFAVLKLMG	0.039	0.207	0.041	0.218	0.442	-1.177	0.207	0.684	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRG	0.099	0.347	0.129	0.380	0.503	-0.993	0.347	0.459	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRGTKF	0.088	0.336	0.129	0.380	0.443	-1.174	0.336	0.473	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
VGRPEWWMDYQ	0.982	0.982	0.904	0.964	1.152	0.204	0.964	0.016	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.976	0.982	0.778	0.908	1.126	0.171	0.908	0.042	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGFG	0.113	0.374	0.238	0.467	0.423	-1.240	0.374	0.428	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGR	0.729	0.851	0.717	0.882	1.128	0.173	0.851	0.070	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGRIG	0.581	0.766	0.206	0.444	0.658	-0.603	0.444	0.353	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VPPVQVSPLIKL	0.807	0.903	0.968	0.977	0.989	-0.015	0.903	0.044	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
VPPVQVSPLIKLGRY	0.413	0.700	0.442	0.660	1.068	0.095	0.660	0.180	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
YGGFLRKYP	0.119	0.375	0.272	0.492	1.417	0.503	0.375	0.426	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFLRKYPK	0.662	0.812	1.000	1.000	0.990	-0.014	0.812	0.090	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFMRF	0.960	0.977	0.717	0.882	0.944	-0.083	0.882	0.054	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.619	0.807	0.657	0.877	1.216	0.282	0.807	0.093	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY(-.98)	0.104	0.354	0.109	0.369	0.588	-0.765	0.354	0.451	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

[1] "There is no significant differentiated features between Torpor and March"

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

October vs Torpor

Full stat

Code

contrast = combo_list[[10]]

df = d5_mod %>%
    dplyr::filter(., Label %in% contrast ) %>%
    droplevels()

temp_d <- df %>%
        mutate(across(-Label, ~ 2^(.) )) %>% # d3_mod is log-scale number, this step will de-log and change data back to linear number
        group_by(Label) %>%
        summarise(across(everything(), mean))

print(paste("Order of Fold Change:", temp_d$Label[1], "over", temp_d$Label[2], sep = " "))

[1] "Order of Fold Change: October over Torpor"

Code

uni_res <- do_univariate(df)

uni_res <- uni_res %>%
        rowwise() %>%
        mutate(padj = min(c(BHT, BHW))) %>%
        # get the lowest padj
        ungroup() %>%
        mutate(`-log10padj` = -log10(padj))

uni_res_annotation = uni_res %>% left_join(., feature_meta, by = c("variable" = "Peptide"))

uni_res_annotation %>% 
        knitr::kable(., digits = 3, "html") %>%
        kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
        kableExtra::scroll_box(width = "100%", height = "500px")

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	Accession	Name	GN
A(+42.01)AYKLVLIRH	0.189	0.243	0.261	0.325	1.403	0.489	0.243	0.615	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHG	0.316	0.384	0.230	0.293	1.412	0.497	0.293	0.534	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)AYKLVLIRHGE	0.004	0.009	0.001	0.002	2.710	1.438	0.002	2.682	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)GQAFRKFLPLFDRVLVER	0.004	0.010	0.001	0.002	2.471	1.305	0.002	2.682	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
A(+42.01)LLRGVFIVAAKR	0.008	0.015	0.003	0.007	2.487	1.314	0.007	2.152	tr|I3N5Y9|I3N5Y9_ICTTR	Acetyl-CoA acyltransferase 2	ACAA2
AADQDLGPEAPPEGVLGA	0.000	0.000	0.000	0.000	0.198	-2.336	0.000	5.358	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.000	0.001	0.000	0.001	0.303	-1.725	0.001	2.954	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALL	0.000	0.001	0.000	0.000	0.149	-2.749	0.000	4.021	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALLRV	0.000	0.000	0.000	0.001	0.177	-2.497	0.000	3.628	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AEALERMFL	0.076	0.106	0.152	0.200	3.584	1.842	0.106	0.974	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
AFQKVVAGVANALSHKYH	0.239	0.294	0.175	0.226	1.259	0.332	0.226	0.646	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
AFVLVLYDELKKVI	0.928	0.937	0.656	0.734	1.591	0.670	0.734	0.134	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
ALNSVAYERNAMQNY	0.006	0.013	0.007	0.014	0.360	-1.473	0.013	1.883	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
ALNSVAYERNAMQNYE	0.000	0.001	0.000	0.000	0.202	-2.307	0.000	3.829	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
APIGLKAVVG	0.830	0.876	0.824	0.870	0.907	-0.141	0.870	0.060	tr|A0A287D563|A0A287D563_ICTTR	Syntaxin binding protein 1	STXBP1
ASWTREPLE	0.000	0.000	0.000	0.000	0.144	-2.797	0.000	5.108	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
ASWTREPLEE	0.005	0.010	0.012	0.021	0.463	-1.111	0.010	2.004	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
DIDTAAKFIGAGAA	0.031	0.048	0.020	0.033	0.528	-0.922	0.033	1.481	tr|I3MKX8|I3MKX8_ICTTR	ATP synthase lipid-binding protein	ATP5MC1
DILGKYVD	0.044	0.066	0.007	0.014	2.123	1.086	0.014	1.850	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
EDEAAWSLDRTQQ	0.000	0.000	0.000	0.000	0.158	-2.658	0.000	4.852	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
EIGDEENSAKFPI(-.98)	0.001	0.002	0.001	0.002	0.343	-1.544	0.002	2.790	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
FLGEAYHHVPESQ	0.006	0.012	0.003	0.007	0.319	-1.647	0.007	2.152	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.000	0.001	0.000	0.000	0.283	-1.823	0.000	3.653	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLVFHSFGGG	0.774	0.839	0.766	0.833	1.290	0.367	0.833	0.079	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
GAAAQSLYIANHAY	0.065	0.092	0.046	0.069	1.488	0.574	0.069	1.159	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
GAEALERMFL	0.043	0.066	0.067	0.096	1.773	0.827	0.066	1.183	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
GAFVLVLYDELKKVI	0.003	0.008	0.007	0.014	0.464	-1.108	0.008	2.109	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
GASLKPEFVDIINAKQ	0.643	0.735	1.000	1.000	1.156	0.209	0.735	0.134	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
GGFMRGL	0.914	0.937	0.941	0.958	0.386	-1.372	0.937	0.028	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
GLQGFLVFH	0.024	0.041	0.031	0.048	1.892	0.920	0.041	1.383	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
KVVAGVANALSHKYH	0.005	0.011	0.002	0.006	3.366	1.751	0.006	2.254	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
LEDEAKELQ	0.105	0.142	0.131	0.177	1.651	0.723	0.142	0.849	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
LENPQPQAPA	0.000	0.000	0.000	0.000	0.201	-2.317	0.000	4.105	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LENPQPQAPARRLLPP	0.000	0.000	0.000	0.000	0.185	-2.434	0.000	4.021	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGVLFNPYYDPLQWKSSRFE	0.001	0.004	0.003	0.007	0.432	-1.212	0.004	2.448	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LQGFLVFH	0.004	0.009	0.001	0.002	3.609	1.852	0.002	2.682	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
M(+42.01)DVFMKGL	0.007	0.013	0.000	0.001	4.505	2.171	0.001	3.128	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
MDELYPVEPEEEANGGEVL	0.000	0.000	0.000	0.000	0.144	-2.792	0.000	3.461	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MDELYPVEPEEEANGGEVLA	0.001	0.002	0.000	0.000	0.153	-2.712	0.000	3.653	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MQIFVKTL	0.065	0.092	0.007	0.014	1.900	0.926	0.014	1.850	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLT	0.753	0.835	0.882	0.906	1.099	0.136	0.835	0.078	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
MQIFVKTLTGK	0.779	0.839	0.603	0.682	1.110	0.150	0.682	0.166	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
PMFVVNTNVPRA	0.744	0.833	0.824	0.870	0.821	-0.284	0.833	0.079	tr|I3N9F5|I3N9F5_ICTTR	Macrophage migration inhibitory factor	MIF
PVNFKLL	0.001	0.004	0.001	0.003	4.944	2.306	0.003	2.532	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
PYQYPAL	0.000	0.000	0.000	0.000	7.913	2.984	0.000	4.327	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
Q(-17.03)EDAELQP	0.000	0.000	0.000	0.000	0.126	-2.990	0.000	4.492	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)EDAELQPR	0.000	0.000	0.000	0.000	0.096	-3.381	0.000	4.764	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)YDRVAELDQLLHY	0.000	0.000	0.000	0.001	0.360	-1.474	0.000	3.618	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
RPKPQQFFGLM(-.98)	0.131	0.173	0.080	0.111	0.585	-0.773	0.111	0.954	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
RTLYGFGG	0.927	0.937	0.882	0.906	1.015	0.022	0.906	0.043	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
S(+42.01)DKPDMAEIEKFDK	0.995	0.995	1.000	1.000	0.993	-0.011	0.995	0.002	tr|A0A287CVS2|A0A287CVS2_ICTTR	Thymosin beta	Tmsb4x
S(+42.01)ILKIHAREIFD	0.003	0.007	0.004	0.009	2.128	1.089	0.007	2.128	tr|I3MIE7|I3MIE7_ICTTR	2-phospho-D-glycerate hydro-lyase	ENO1
SAMLIQKL	0.762	0.837	0.370	0.446	1.209	0.274	0.446	0.351	tr|I3M435|I3M435_ICTTR	Acetyl-CoA acetyltransferase 1	ACAT1
SAVISLEGKPL	0.581	0.685	0.882	0.906	1.077	0.107	0.685	0.164	tr|I3MY03|I3MY03_ICTTR	Cofilin, non-muscle isoform	CFL1
SESLFVSNHAY	0.002	0.006	0.006	0.012	1.640	0.713	0.006	2.247	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SFFAVMGA	0.629	0.727	0.503	0.580	0.893	-0.163	0.580	0.236	tr|A0A287CVH5|A0A287CVH5_ICTTR	Polypyrimidine tract binding protein 2	PTBP2
SGFAAPFFIVRHQLLKK	0.606	0.707	0.603	0.682	2.235	1.160	0.682	0.166	tr|A0A287CU43|A0A287CU43_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967835
SGFTSLLMERL	0.825	0.876	0.710	0.780	0.558	-0.841	0.780	0.108	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SGPFGQIFRPDNFVFGQ	0.928	0.937	0.710	0.780	1.110	0.151	0.780	0.108	tr|I3NEP5|I3NEP5_ICTTR	Tubulin beta chain	TUBB2B
SGSAKVAFSAIRSTNH	0.002	0.005	0.000	0.000	0.269	-1.896	0.000	3.653	tr|I3MWG7|I3MWG7_ICTTR	GST class-pi	GSTP1
SHLGGAVF	0.004	0.010	0.006	0.012	4.750	2.248	0.010	2.004	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
SIGRFFG	0.018	0.032	0.046	0.069	1.733	0.793	0.032	1.496	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGG	0.000	0.001	0.000	0.001	14.034	3.811	0.001	3.128	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGGDRG	0.000	0.001	0.000	0.000	6.722	2.749	0.000	3.461	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIYPAPQVS	0.086	0.118	0.056	0.082	1.180	0.238	0.082	1.088	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
SLDKFLA	0.000	0.000	0.000	0.000	10.938	3.451	0.000	4.021	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLDKFLASVSTVLTSKYR	0.010	0.018	0.010	0.017	3.349	1.744	0.017	1.764	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLFVSNHAY	0.000	0.000	0.000	0.000	3.554	1.829	0.000	4.818	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SLKPEFVDIINAKQ	0.027	0.044	0.031	0.048	1.434	0.520	0.044	1.356	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
SLSAASPPMTEAGTPRRF	0.000	0.000	0.000	0.000	0.145	-2.789	0.000	5.358	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SLYIANHAY	0.001	0.004	0.002	0.006	2.504	1.324	0.004	2.440	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
SPEPEAAAAVPRRL	0.001	0.003	0.001	0.002	0.243	-2.041	0.002	2.682	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SPQLEDEAKEL	0.000	0.000	0.000	0.000	0.192	-2.378	0.000	5.876	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.002	0.005	0.000	0.000	0.231	-2.112	0.000	3.653	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SSPETLISDLLMRESTENVPRTRLEDPSMW	0.000	0.001	0.000	0.000	0.154	-2.698	0.000	3.461	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY
STLHLVLRLRGG	0.008	0.016	0.010	0.017	1.773	0.826	0.016	1.797	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
SVLISLKQAPLVH	0.061	0.088	0.056	0.082	1.817	0.862	0.082	1.088	tr|A0A287D1C0|A0A287D1C0_ICTTR	Clathrin light chain	CLTA
SVPRGEAAGAVQELARALAHLLEAERQE	0.000	0.001	0.000	0.001	0.289	-1.790	0.001	3.292	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SVSTVLTSKYR	0.228	0.284	0.080	0.111	1.754	0.811	0.111	0.954	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TAYAIYELAKA	0.010	0.018	0.016	0.027	2.766	1.468	0.018	1.745	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TAYAIYELAKASFPKKQD	0.693	0.784	0.456	0.538	1.117	0.160	0.538	0.269	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TDYLMKIL	0.054	0.080	0.095	0.130	2.161	1.112	0.080	1.096	tr|I3MNL1|I3MNL1_ICTTR	Actin beta	ACTB
TGLQGFLVFH	0.027	0.044	0.010	0.017	1.552	0.634	0.017	1.764	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TGLQGFLVFHSFGGG	0.387	0.466	0.331	0.408	1.276	0.351	0.408	0.390	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
THYKLVPHQFAH	0.002	0.006	0.000	0.001	3.036	1.602	0.001	3.287	tr|I3MGG0|I3MGG0_ICTTR	Cytochrome c oxidase polypeptide Vb	LOC101965209
TIDFPEFL	0.007	0.013	0.006	0.012	2.758	1.464	0.012	1.931	tr|I3MRD3|I3MRD3_ICTTR	Calmodulin	CALM1
TLHLVLRLRGG	0.019	0.033	0.020	0.033	2.742	1.455	0.033	1.481	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
TLSKIFKLGGKDSRSGSPMARR	0.058	0.086	0.152	0.200	1.510	0.595	0.086	1.066	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
TLYGFGG	0.001	0.003	0.001	0.002	2.339	1.226	0.002	2.682	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TPAVHASLDKFLA	0.109	0.145	0.456	0.538	1.370	0.454	0.145	0.838	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPAVHASLDKFLASVSTVLTSKYR	0.150	0.195	0.175	0.226	1.809	0.855	0.195	0.710	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TPEAQAAFQKVVAGVANALSHKYH	0.000	0.000	0.000	0.000	4.973	2.314	0.000	4.021	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
TSLLMERL	0.040	0.062	0.038	0.058	3.399	1.765	0.058	1.233	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
TTMIIDHVVPEPG	0.853	0.893	0.824	0.870	1.075	0.104	0.870	0.060	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TVVYGEPITA	0.000	0.000	0.000	0.000	20.320	4.345	0.000	4.021	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TYFPHFDL	0.005	0.010	0.010	0.017	6.371	2.671	0.010	2.004	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYFPHFDLSHG	0.025	0.042	0.025	0.041	5.062	2.340	0.041	1.391	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYNFAVLKLMG	0.031	0.048	0.012	0.021	1.853	0.890	0.021	1.668	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRG	0.011	0.020	0.007	0.014	3.995	1.998	0.014	1.850	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRGTKF	0.538	0.642	0.503	0.580	1.242	0.313	0.580	0.236	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
VGRPEWWMDYQ	0.000	0.001	0.000	0.000	0.239	-2.067	0.000	4.021	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.006	0.013	0.003	0.007	0.400	-1.321	0.007	2.152	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VKVGVNGFG	0.222	0.280	0.370	0.446	0.876	-0.191	0.280	0.553	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGR	0.213	0.271	0.261	0.325	1.308	0.387	0.271	0.566	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VKVGVNGFGRIG	0.080	0.111	0.067	0.096	0.733	-0.448	0.096	1.019	tr|A0A287D887|A0A287D887_ICTTR	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH
VPPVQVSPLIKL	0.027	0.045	0.031	0.048	1.765	0.820	0.045	1.351	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
VPPVQVSPLIKLGRY	0.000	0.000	0.000	0.000	3.559	1.831	0.000	3.678	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
YGGFLRKYP	0.000	0.000	0.000	0.000	0.152	-2.718	0.000	5.876	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFLRKYPK	0.000	0.000	0.000	0.001	0.353	-1.503	0.000	3.618	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFMRF	0.001	0.002	0.000	0.001	0.247	-2.020	0.001	2.954	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.000	0.001	0.001	0.002	0.338	-1.565	0.001	2.915	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY(-.98)	0.000	0.000	0.000	0.000	0.091	-3.464	0.000	4.644	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY

Significant stat

Code

# get DE features only tibble
uni_res_filt <- uni_res %>%
        dplyr::filter(BHT < FDR & BHW < FDR) %>%
        mutate(status = case_when(`FC(log2)` < - 0.6 ~ "Down",
                                  `FC(log2)` > 0.6 ~ "Up") )

if (nrow(uni_res_filt) == 0){
        print(paste("There is no significant differentiated features between",
                    temp_d$Label[2], "and", temp_d$Label[1], sep = " "))
} else {
        uni_res_filt = uni_res_filt %>%
                left_join(., feature_meta, by = c("variable" = "Peptide"))
        
        uni_res_filt %>% 
                knitr::kable(., digits = 3, "html") %>%
                kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
                kableExtra::scroll_box(width = "100%", height = "500px")
}

variable	pT	BHT	pW	BHW	FC(lin)	FC(log2)	padj	-log10padj	status	Accession	Name	GN
A(+42.01)AYKLVLIRHGE	0.004	0.009	0.001	0.002	2.710	1.438	0.002	2.682	Up	tr|I3NCB7|I3NCB7_ICTTR	Phosphoglycerate mutase	PGAM1
A(+42.01)GQAFRKFLPLFDRVLVER	0.004	0.010	0.001	0.002	2.471	1.305	0.002	2.682	Up	tr|I3N0V0|I3N0V0_ICTTR	10 kDa heat shock protein, mitochondrial	HSPE1
A(+42.01)LLRGVFIVAAKR	0.008	0.015	0.003	0.007	2.487	1.314	0.007	2.152	Up	tr|I3N5Y9|I3N5Y9_ICTTR	Acetyl-CoA acyltransferase 2	ACAA2
AADQDLGPEAPPEGVLGA	0.000	0.000	0.000	0.000	0.198	-2.336	0.000	5.358	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGAL	0.000	0.001	0.000	0.001	0.303	-1.725	0.001	2.954	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALL	0.000	0.001	0.000	0.000	0.149	-2.749	0.000	4.021	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
AADQDLGPEAPPEGVLGALLRV	0.000	0.000	0.000	0.001	0.177	-2.497	0.000	3.628	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
ALNSVAYERNAMQNY	0.006	0.013	0.007	0.014	0.360	-1.473	0.013	1.883	Down	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
ALNSVAYERNAMQNYE	0.000	0.001	0.000	0.000	0.202	-2.307	0.000	3.829	Down	tr|A0A287CUU0|A0A287CUU0_ICTTR	Protachykinin-1	TAC1
ASWTREPLE	0.000	0.000	0.000	0.000	0.144	-2.797	0.000	5.108	Down	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
ASWTREPLEE	0.005	0.010	0.012	0.021	0.463	-1.111	0.010	2.004	Down	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
DIDTAAKFIGAGAA	0.031	0.048	0.020	0.033	0.528	-0.922	0.033	1.481	Down	tr|I3MKX8|I3MKX8_ICTTR	ATP synthase lipid-binding protein	ATP5MC1
EDEAAWSLDRTQQ	0.000	0.000	0.000	0.000	0.158	-2.658	0.000	4.852	Down	tr|I3NCI2|I3NCI2_ICTTR	Pro-thyrotropin-releasing hormone	TRH
EIGDEENSAKFPI(-.98)	0.001	0.002	0.001	0.002	0.343	-1.544	0.002	2.790	Down	tr|I3MQ49|I3MQ49_ICTTR	Pro-melanin concentrating hormone	PMCH
FLGEAYHHVPESQ	0.006	0.012	0.003	0.007	0.319	-1.647	0.007	2.152	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
FLGEAYHHVPESQRD	0.000	0.001	0.000	0.000	0.283	-1.823	0.000	3.653	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
GAFVLVLYDELKKVI	0.003	0.008	0.007	0.014	0.464	-1.108	0.008	2.109	Down	tr|I3MHK9|I3MHK9_ICTTR	ADP/ATP translocase	SLC25A7
GLQGFLVFH	0.024	0.041	0.031	0.048	1.892	0.920	0.041	1.383	Up	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
KVVAGVANALSHKYH	0.005	0.011	0.002	0.006	3.366	1.751	0.006	2.254	Up	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
LENPQPQAPA	0.000	0.000	0.000	0.000	0.201	-2.317	0.000	4.105	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LENPQPQAPARRLLPP	0.000	0.000	0.000	0.000	0.185	-2.434	0.000	4.021	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
LGVLFNPYYDPLQWKSSRFE	0.001	0.004	0.003	0.007	0.432	-1.212	0.004	2.448	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
LQGFLVFH	0.004	0.009	0.001	0.002	3.609	1.852	0.002	2.682	Up	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
M(+42.01)DVFMKGL	0.007	0.013	0.000	0.001	4.505	2.171	0.001	3.128	Up	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
MDELYPVEPEEEANGGEVL	0.000	0.000	0.000	0.000	0.144	-2.792	0.000	3.461	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
MDELYPVEPEEEANGGEVLA	0.001	0.002	0.000	0.000	0.153	-2.712	0.000	3.653	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
PVNFKLL	0.001	0.004	0.001	0.003	4.944	2.306	0.003	2.532	Up	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
PYQYPAL	0.000	0.000	0.000	0.000	7.913	2.984	0.000	4.327	Up	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
Q(-17.03)EDAELQP	0.000	0.000	0.000	0.000	0.126	-2.990	0.000	4.492	Down	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)EDAELQPR	0.000	0.000	0.000	0.000	0.096	-3.381	0.000	4.764	Down	tr|I3MEC5|I3MEC5_ICTTR	Cocaine- and amphetamine-regulated transcript protein	CARTPT
Q(-17.03)YDRVAELDQLLHY	0.000	0.000	0.000	0.001	0.360	-1.474	0.000	3.618	Down	tr|I3NBA1|I3NBA1_ICTTR	Secretogranin-1	CHGB
S(+42.01)ILKIHAREIFD	0.003	0.007	0.004	0.009	2.128	1.089	0.007	2.128	Up	tr|I3MIE7|I3MIE7_ICTTR	2-phospho-D-glycerate hydro-lyase	ENO1
SESLFVSNHAY	0.002	0.006	0.006	0.012	1.640	0.713	0.006	2.247	Up	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SGSAKVAFSAIRSTNH	0.002	0.005	0.000	0.000	0.269	-1.896	0.000	3.653	Down	tr|I3MWG7|I3MWG7_ICTTR	GST class-pi	GSTP1
SHLGGAVF	0.004	0.010	0.006	0.012	4.750	2.248	0.010	2.004	Up	tr|I3N4D8|I3N4D8_ICTTR	Beta-synuclein	SNCB
SIGRFFGG	0.000	0.001	0.000	0.001	14.034	3.811	0.001	3.128	Up	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SIGRFFGGDRG	0.000	0.001	0.000	0.000	6.722	2.749	0.000	3.461	Up	tr|A0A287CZ39|A0A287CZ39_ICTTR	Myelin basic protein	MBP
SLDKFLA	0.000	0.000	0.000	0.000	10.938	3.451	0.000	4.021	Up	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLDKFLASVSTVLTSKYR	0.010	0.018	0.010	0.017	3.349	1.744	0.017	1.764	Up	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
SLFVSNHAY	0.000	0.000	0.000	0.000	3.554	1.829	0.000	4.818	Up	tr|A0A287D688|A0A287D688_ICTTR	Fructose-bisphosphate aldolase	ALDOA
SLKPEFVDIINAKQ	0.027	0.044	0.031	0.048	1.434	0.520	0.044	1.356	NA	tr|I3N8X9|I3N8X9_ICTTR	Triosephosphate isomerase	Tpi1
SLSAASPPMTEAGTPRRF	0.000	0.000	0.000	0.000	0.145	-2.789	0.000	5.358	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SLYIANHAY	0.001	0.004	0.002	0.006	2.504	1.324	0.004	2.440	Up	tr|I3LWU9|I3LWU9_ICTTR	Fructose-bisphosphate aldolase	ALDOC
SPEPEAAAAVPRRL	0.001	0.003	0.001	0.002	0.243	-2.041	0.002	2.682	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
SPQLEDEAKEL	0.000	0.000	0.000	0.000	0.192	-2.378	0.000	5.876	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SPQLEDEAKELQ	0.002	0.005	0.000	0.000	0.231	-2.112	0.000	3.653	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
SSPETLISDLLMRESTENVPRTRLEDPSMW	0.000	0.001	0.000	0.000	0.154	-2.698	0.000	3.461	Down	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY
STLHLVLRLRGG	0.008	0.016	0.010	0.017	1.773	0.826	0.016	1.797	Up	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
SVPRGEAAGAVQELARALAHLLEAERQE	0.000	0.001	0.000	0.001	0.289	-1.790	0.001	3.292	Down	tr|I3NGD6|I3NGD6_ICTTR	ProSAAS	PCSK1N
TAYAIYELAKA	0.010	0.018	0.016	0.027	2.766	1.468	0.018	1.745	Up	tr|I3M0L6|I3M0L6_ICTTR	Cytochrome c oxidase subunit 7A2, mitochondrial	LOC101966864
TGLQGFLVFH	0.027	0.044	0.010	0.017	1.552	0.634	0.017	1.764	Up	tr|I3NHW3|I3NHW3_ICTTR	Tubulin alpha chain	TUB4A
THYKLVPHQFAH	0.002	0.006	0.000	0.001	3.036	1.602	0.001	3.287	Up	tr|I3MGG0|I3MGG0_ICTTR	Cytochrome c oxidase polypeptide Vb	LOC101965209
TIDFPEFL	0.007	0.013	0.006	0.012	2.758	1.464	0.012	1.931	Up	tr|I3MRD3|I3MRD3_ICTTR	Calmodulin	CALM1
TLHLVLRLRGG	0.019	0.033	0.020	0.033	2.742	1.455	0.033	1.481	Up	tr|I3MDS7|I3MDS7_ICTTR	Ubiquitin carboxyl extension protein 80	RPS27A
TLYGFGG	0.001	0.003	0.001	0.002	2.339	1.226	0.002	2.682	Up	tr|I3N7M0|I3N7M0_ICTTR	Histone H4	LOC106145262
TPEAQAAFQKVVAGVANALSHKYH	0.000	0.000	0.000	0.000	4.973	2.314	0.000	4.021	Up	tr|A0A287CUK4|A0A287CUK4_ICTTR	Hemoglobin subunit beta-S/F-like	LOC101967841
TVVYGEPITA	0.000	0.000	0.000	0.000	20.320	4.345	0.000	4.021	Up	tr|I3M3I9|I3M3I9_ICTTR	Dihydropyrimidinase-related protein 2	DPYSL2
TYFPHFDL	0.005	0.010	0.010	0.017	6.371	2.671	0.010	2.004	Up	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYFPHFDLSHG	0.025	0.042	0.025	0.041	5.062	2.340	0.041	1.391	Up	tr|A0A287D1R9|A0A287D1R9_ICTTR	Hemoglobin subunit alpha	LOC101956162
TYNFAVLKLMG	0.031	0.048	0.012	0.021	1.853	0.890	0.021	1.668	Up	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
TYNFAVLKLMGRG	0.011	0.020	0.007	0.014	3.995	1.998	0.014	1.850	Up	tr|I3M3J2|I3M3J2_ICTTR	Proteolipid protein 1	PLP1
VGRPEWWMDYQ	0.000	0.001	0.000	0.000	0.239	-2.067	0.000	4.021	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
VKMALQQEGFD	0.006	0.013	0.003	0.007	0.400	-1.321	0.007	2.152	Down	tr|I3MEG8|I3MEG8_ICTTR	Proprotein convertase subtilisin/kexin type 2	PCSK2
VPPVQVSPLIKL	0.027	0.045	0.031	0.048	1.765	0.820	0.045	1.351	Up	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
VPPVQVSPLIKLGRY	0.000	0.000	0.000	0.000	3.559	1.831	0.000	3.678	Up	tr|I3NFX8|I3NFX8_ICTTR	ATP synthase subunit e, mitochondrial	ATP5ME
YGGFLRKYP	0.000	0.000	0.000	0.000	0.152	-2.718	0.000	5.876	Down	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFLRKYPK	0.000	0.000	0.000	0.001	0.353	-1.503	0.000	3.618	Down	tr|I3MVB5|I3MVB5_ICTTR	Proenkephalin-B	PDYN
YGGFMRF	0.001	0.002	0.000	0.001	0.247	-2.020	0.001	2.954	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YGGFMRGL	0.000	0.001	0.001	0.002	0.338	-1.565	0.001	2.915	Down	tr|I3MGR7|I3MGR7_ICTTR	Proenkephalin-A	PENK
YPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY(-.98)	0.000	0.000	0.000	0.000	0.091	-3.464	0.000	4.644	Down	tr|I3NFR3|I3NFR3_ICTTR	Pro-neuropeptide Y	NPY

Volcano plot

Code

# volcano plot
volcano_plot(uni_res_annotation, feature_col = "variable", fdr = FDR, log2fc = LOG2FC, save = FALSE)

Heatmap

Code

# heatmap
anno <- data.frame(Label = as.factor(t(d5)[, "class"])) %>%
        filter(Label %in% contrast ) %>%
        droplevels()

hm <- d5[-1, d5[1,] %in% contrast ] %>%
        rownames_to_column("variable") %>%
        mutate(across(-variable, as.numeric)) #%>%
        #left_join(., feature_meta, by = c("variable" = "Feature"))

# select color palette of current pair
selected_colors = anno_colors[levels(anno[[1]])]

heatmap(hm, feature_col = "variable", sample_anno = anno, sample_colors = selected_colors, feature_anno = feature_meta, feature_label = "Peptide", rowname_switch = TRUE, save = FALSE)

All group heatmaps

Ordered

Code

# for ordered column without clustering samples

# data wrangling for all group heatmap
norm_d2 = t(norm_d1) %>% as.data.frame()

norm_d3 = norm_d2 %>%
        arrange(factor(class, levels = col_order))

norm_d4 = t(norm_d3) %>% as.data.frame()
norm_d4_mod = norm_d4[-1,] %>%
        as.data.frame() %>%
        rownames_to_column(., var = "rowname") %>%
        mutate(across(-rowname, as.numeric)) %>%
        column_to_rownames(., var = "rowname")

anno <- data.frame(Label = as.factor(t(norm_d4)[, "class"]))
# levels() only change the name of each level, it doesn't reorder
# factor() to reorder factor level
anno$Label = factor(anno$Label, levels = col_order)
#levels(anno$Label)

rownames(norm_d4_mod) = feature_name$name

heatmap(norm_d4_mod, sample_anno = anno, sample_anno_col = "Label", sample_colors = anno_colors, feature_anno = feature_meta, feature_label = "Peptide", cluster_col_switch = FALSE, rowname_switch = TRUE, save = FALSE)

Clustered

Code

heatmap(norm_d4_mod, sample_anno = anno, sample_anno_col = "Label", sample_colors = anno_colors, feature_anno = feature_meta, feature_label = "Peptide", cluster_col_switch = TRUE, rowname_switch = TRUE, save = FALSE)

Reproducibility

The amount of time took to generate the report:

Code

Sys.time() - start_time

Time difference of 2.904352 mins

R session information:

Code

sessionInfo()

R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] plotly_4.10.1       VennDiagram_1.7.3   futile.logger_1.4.3
 [4] wesanderson_0.3.6   RColorBrewer_1.1-3  extrafont_0.19     
 [7] pheatmap_1.0.12     ggrepel_0.9.3       ropls_1.28.2       
[10] ProteoMM_1.14.0     pROC_1.18.2         pcaMethods_1.88.0  
[13] Biobase_2.56.0      BiocGenerics_0.42.0 proBatch_1.11.0    
[16] cowplot_1.1.1       impute_1.70.0       statTarget_1.26.0  
[19] knitr_1.43.1        lubridate_1.9.2     forcats_1.0.0      
[22] stringr_1.5.0       dplyr_1.1.2         purrr_1.0.1        
[25] readr_2.1.4         tidyr_1.3.0         tibble_3.2.1       
[28] ggplot2_3.4.2       tidyverse_2.0.0    

loaded via a namespace (and not attached):
  [1] backports_1.4.1             Hmisc_5.1-0                
  [3] qqman_0.1.8                 corrplot_0.92              
  [5] systemfonts_1.0.4           plyr_1.8.8                 
  [7] lazyeval_0.2.2              splines_4.2.1              
  [9] BiocParallel_1.30.4         GenomeInfoDb_1.32.4        
 [11] sva_3.44.0                  digest_0.6.31              
 [13] foreach_1.5.2               htmltools_0.5.5            
 [15] viridis_0.6.3               GO.db_3.15.0               
 [17] fansi_1.0.4                 ggfortify_0.4.16           
 [19] magrittr_2.0.3              checkmate_2.2.0            
 [21] memoise_2.0.1               cluster_2.1.4              
 [23] doParallel_1.0.17           tzdb_0.4.0                 
 [25] limma_3.52.4                fastcluster_1.2.3          
 [27] Biostrings_2.64.1           annotate_1.74.0            
 [29] matrixStats_0.63.0          svglite_2.1.1              
 [31] extrafontdb_1.0             timechange_0.2.0           
 [33] pdist_1.2.1                 colorspace_2.1-0           
 [35] rvest_1.0.3                 blob_1.2.4                 
 [37] rrcov_1.7-2                 xfun_0.39                  
 [39] crayon_1.5.2                RCurl_1.98-1.12            
 [41] jsonlite_1.8.4              genefilter_1.78.0          
 [43] lme4_1.1-33                 survival_3.5-5             
 [45] iterators_1.0.14            glue_1.6.2                 
 [47] kableExtra_1.3.4            gtable_0.3.3               
 [49] zlibbioc_1.42.0             XVector_0.36.0             
 [51] webshot_0.5.4               DelayedArray_0.22.0        
 [53] Rttf2pt1_1.3.12             DEoptimR_1.0-13            
 [55] scales_1.2.1                futile.options_1.0.1       
 [57] vsn_3.64.0                  mvtnorm_1.1-3              
 [59] DBI_1.1.3                   edgeR_3.38.4               
 [61] Rcpp_1.0.10                 MultiDataSet_1.24.0        
 [63] viridisLite_0.4.2           xtable_1.8-4               
 [65] htmlTable_2.4.1             foreign_0.8-84             
 [67] bit_4.0.5                   preprocessCore_1.58.0      
 [69] Formula_1.2-5               stats4_4.2.1               
 [71] htmlwidgets_1.6.2           httr_1.4.6                 
 [73] calibrate_1.7.7             farver_2.1.1               
 [75] pkgconfig_2.0.3             XML_3.99-0.14              
 [77] nnet_7.3-19                 locfit_1.5-9.7             
 [79] utf8_1.2.3                  dynamicTreeCut_1.63-1      
 [81] labeling_0.4.2              tidyselect_1.2.0           
 [83] rlang_1.1.1                 reshape2_1.4.4             
 [85] AnnotationDbi_1.58.0        munsell_0.5.0              
 [87] tools_4.2.1                 cachem_1.0.8               
 [89] cli_3.6.1                   generics_0.1.3             
 [91] RSQLite_2.3.1               pls_2.8-2                  
 [93] evaluate_0.21               fastmap_1.1.1              
 [95] yaml_2.3.7                  bit64_4.0.5                
 [97] robustbase_0.95-1           randomForest_4.7-1.1       
 [99] ROC_1.72.0                  KEGGREST_1.36.3            
[101] nlme_3.1-162                formatR_1.14               
[103] xml2_1.3.4                  compiler_4.2.1             
[105] rstudioapi_0.14             png_0.1-8                  
[107] affyio_1.66.0               pcaPP_2.0-3                
[109] stringi_1.7.12              highr_0.10                 
[111] lattice_0.21-8              Matrix_1.5-4               
[113] nloptr_2.0.3                vctrs_0.6.2                
[115] pillar_1.9.0                lifecycle_1.0.3            
[117] BiocManager_1.30.20         pvca_1.36.0                
[119] data.table_1.14.8           bitops_1.0-7               
[121] GenomicRanges_1.48.0        R6_2.5.1                   
[123] affy_1.74.0                 gridExtra_2.3              
[125] IRanges_2.30.1              codetools_0.2-19           
[127] lambda.r_1.2.4              boot_1.3-28.1              
[129] MASS_7.3-60                 SummarizedExperiment_1.26.1
[131] withr_2.5.0                 S4Vectors_0.34.0           
[133] GenomeInfoDbData_1.2.8      MultiAssayExperiment_1.22.0
[135] mgcv_1.8-42                 parallel_4.2.1             
[137] hms_1.1.3                   rpart_4.1.19               
[139] minqa_1.2.5                 rmarkdown_2.21             
[141] MatrixGenerics_1.8.1        WGCNA_1.72-1               
[143] base64enc_0.1-3