# HG changeset patch
# User iuc
# Date 1686167330 0
# Node ID 28e29a3d0eda272ac9c31fa3a393ccc172fadc5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea commit 5c1b8a2b105a80e236f88e71a743147d79925ac4
diff -r 000000000000 -r 28e29a3d0eda macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Jun 07 19:48:50 2023 +0000
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+
+ 1.8.0
+ 0
+ 20.05
+
+
+ bioconductor-multigsea
+ r-argparse
+ bioconductor-metaboliteidmapping
+ bioconductor-org.Hs.eg.db
+ bioconductor-org.Mm.eg.db
+ bioconductor-org.Rn.eg.db
+ bioconductor-org.Cf.eg.db
+ bioconductor-org.Bt.eg.db
+ bioconductor-org.Ss.eg.db
+ bioconductor-org.Gg.eg.db
+ bioconductor-org.Xl.eg.db
+ bioconductor-org.Dr.eg.db
+ bioconductor-org.Dm.eg.db
+ bioconductor-org.Ce.eg.db
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+ doi:10.1186/s12859-020-03910-x.
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+ multiGSEA
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diff -r 000000000000 -r 28e29a3d0eda multiGSEA.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/multiGSEA.R Wed Jun 07 19:48:50 2023 +0000
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+library(multiGSEA,
+ quietly = TRUE,
+ warn.conflicts = FALSE)
+library(argparse, quietly = TRUE, warn.conflicts = FALSE)
+
+################################################################################
+### Input Processing
+################################################################################
+
+
+# Collect arguments from command line
+parser <- ArgumentParser(description = "multiGSEA R script")
+
+parser$add_argument("--transcriptomics", required = FALSE,
+ help = "Transcriptomics data")
+parser$add_argument(
+ "--transcriptome_ids",
+ required = FALSE,
+ help = "Transcriptomics ids",
+ default = "SYMBOL"
+)
+parser$add_argument("--proteomics", required = FALSE,
+ help = "Proteomics data")
+parser$add_argument(
+ "--proteome_ids",
+ required = FALSE,
+ help = "Proteomics ids",
+ default = "SYMBOL"
+)
+parser$add_argument("--metabolomics", required = FALSE,
+ help = "Metabolomics data")
+parser$add_argument(
+ "--metabolome_ids",
+ required = FALSE,
+ help = "Metabolomics ids",
+ default = "HMDB"
+)
+parser$add_argument("--organism", required = TRUE,
+ help = "Organism")
+parser$add_argument("--combine_pvalues", required = TRUE,
+ help = "Combine p-values method")
+parser$add_argument("--padj_method", required = TRUE,
+ help = "P-adjustment method")
+parser$add_argument("--databases",
+ required = TRUE,
+ help = "Pathway databases")
+
+args <- parser$parse_args()
+
+## ----Load library-------------------------------------------------------------
+
+organism_mapping <- c(
+ "hsapiens" = "org.Hs.eg.db",
+ "mmusculus" = "org.Mm.eg.db",
+ "rnorvegicus" = "org.Rn.eg.db",
+ "cfamiliaris" = "org.Cf.eg.db",
+ "btaurus" = "org.Bt.eg.db",
+ "sscrofa" = "org.Ss.eg.db",
+ "ggallus" = "org.Gg.eg.db",
+ "drerio" = "org.Xl.eg.db",
+ "xlaevis" = "org.Dr.eg.db",
+ "dmelanogaster" = "org.Dm.eg.db",
+ "celegans" = "org.Ce.eg.db"
+)
+
+library(organism_mapping[args$organism], character.only = TRUE)
+
+
+## ----Load omics data----------------------------------------------------------
+
+layer <- c()
+
+if (!is.null(args$transcriptomics)) {
+ transcriptome <- read.csv(
+ args$transcriptomics,
+ header = TRUE,
+ sep = "\t",
+ dec = "."
+ )
+ layer <- append(layer, "transcriptome")
+}
+
+if (!is.null(args$proteomics)) {
+ proteome <- read.csv(args$proteomics,
+ header = TRUE,
+ sep = "\t",
+ dec = ".")
+ layer <- append(layer, "proteome")
+}
+
+if (!is.null(args$metabolomics)) {
+ metabolome <- read.csv(args$metabolomics,
+ header = TRUE,
+ sep = "\t",
+ dec = ".")
+ layer <- append(layer, "metabolome")
+}
+
+## ----rank_features------------------------------------------------------------
+
+# create data structure
+omics_data <- initOmicsDataStructure(layer)
+
+## add transcriptome layer
+if (!is.null(args$transcriptomics)) {
+ omics_data$transcriptome <- rankFeatures(transcriptome$logFC,
+ transcriptome$pValue)
+ names(omics_data$transcriptome) <- transcriptome$Symbol
+}
+
+## add proteome layer
+if (!is.null(args$proteomics)) {
+ omics_data$proteome <- rankFeatures(proteome$logFC, proteome$pValue)
+ names(omics_data$proteome) <- proteome$Symbol
+}
+
+## add metabolome layer
+## HMDB features have to be updated to the new HMDB format
+if (!is.null(args$metabolomics)) {
+ omics_data$metabolome <-
+ rankFeatures(metabolome$logFC, metabolome$pValue)
+ names(omics_data$metabolome) <- metabolome$HMDB
+ names(omics_data$metabolome) <- gsub("HMDB", "HMDB00",
+ names(omics_data$metabolome))
+}
+
+
+## remove NA's and sort feature ranks
+omics_data <- lapply(omics_data, function(vec) {
+ sort(vec[!is.na(vec)])
+})
+
+## ----Pathway definitions------------------------------------------------------
+
+pathways <-
+ getMultiOmicsFeatures(
+ dbs = unlist(strsplit(args$databases, ",", fixed = TRUE)),
+ layer = layer,
+ returnTranscriptome = args$transcriptome_ids,
+ returnProteome = args$proteome_ids,
+ returnMetabolome = args$metabolome_ids,
+ organism = args$organism,
+ useLocal = FALSE
+ )
+
+## ----calculate enrichment-----------------------------------------------------
+
+enrichment_scores <-
+ multiGSEA(pathways, omics_data)
+
+## ----combine_pvalues----------------------------------------------------------
+
+df <- extractPvalues(enrichmentScores = enrichment_scores,
+ pathwayNames = names(pathways[[1]]))
+
+df$combined_pval <-
+ combinePvalues(df, method = args$combine_pvalues)
+df$combined_padj <-
+ p.adjust(df$combined_pval, method = args$padj_method)
+
+df <- cbind(data.frame(pathway = names(pathways[[1]])), df)
+
+## ----Write output-------------------------------------------------------------
+
+write.table(
+ df,
+ file = "results.tsv",
+ quote = FALSE,
+ sep = "\t",
+ col.names = TRUE,
+ row.names = FALSE
+)
diff -r 000000000000 -r 28e29a3d0eda multigsea.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/multigsea.xml Wed Jun 07 19:48:50 2023 +0000
@@ -0,0 +1,295 @@
+
+ GSEA-based pathway enrichment analysis for multi-omics data
+
+ macros.xml
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diff -r 000000000000 -r 28e29a3d0eda test-data/metabolome.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/metabolome.tsv Wed Jun 07 19:48:50 2023 +0000
@@ -0,0 +1,4882 @@
+HMDB logFC pValue adj.pValue
+HMDB00042 -0.0184063243797361 0.0393850546294737 0.0715518519158232
+HMDB03344 -0.0184063243797361 0.0393850546294737 0.0715518519158232
+HMDB00820 -0.0809343580426596 1.29769217171408e-4 4.58544936100836e-4
+HMDB00863 -0.0809343580426596 1.29769217171408e-4 4.58544936100836e-4
+HMDB06853 -0.0831995371926642 7.40216146766902e-4 0.00215316434714817
+HMDB13785 -0.0831995371926642 7.40216146766902e-4 0.00215316434714817
+HMDB34233 -0.00934945638356588 0.484191596837843 0.563096302375954
+HMDB04296 0.00215711905157612 0.64915129798144 0.715748893346706
+HMDB01167 -0.0939571203141245 5.38210660833356e-16 1.66519116579047e-14
+HMDB06112 -0.0939571203141245 5.38210660833356e-16 1.66519116579047e-14
+HMDB31647 -0.0939571203141245 5.38210660833356e-16 1.66519116579047e-14
+HMDB01106 -0.0347432207851242 0.0326943530012331 0.0615884398787066
+HMDB01888 -0.0347432207851242 0.0326943530012331 0.0615884398787066
+HMDB02134 -0.0347432207851242 0.0326943530012331 0.0615884398787066
+HMDB60177 -0.0347432207851242 0.0326943530012331 0.0615884398787066
+HMDB00119 -0.0937072233758816 4.84523409644223e-5 1.85280300092416e-4
+HMDB00237 -0.0104041409570339 0.208849892788836 0.290116653792384
+HMDB03052 -0.0104041409570339 0.208849892788836 0.290116653792384
+HMDB03453 -0.0104041409570339 0.208849892788836 0.290116653792384
+HMDB06458 -0.0104041409570339 0.208849892788836 0.290116653792384
+HMDB06961 -0.0104041409570339 0.208849892788836 0.290116653792384
+HMDB31229 -0.0104041409570339 0.208849892788836 0.290116653792384
+HMDB31523 -0.0104041409570339 0.208849892788836 0.290116653792384
+HMDB00123 -0.0502655895772399 6.50206470716199e-14 1.20701964836589e-12
+HMDB14691 -0.0502655895772399 6.50206470716199e-14 1.20701964836589e-12
+HMDB31239 -0.0502655895772399 6.50206470716199e-14 1.20701964836589e-12
+HMDB00115 -0.0268586005818108 0.105120388723111 0.163112335693459
+HMDB31608 -0.0268586005818108 0.105120388723111 0.163112335693459
+HMDB13860 -0.00871020591739047 0.00616386659553615 0.0143682826348
+HMDB02039 0.0171869600117898 0.0390684076240339 0.0712300789002475
+HMDB60427 0.0171869600117898 0.0390684076240339 0.0712300789002475
+HMDB00549 -0.0457401508672373 1.59320308480663e-8 1.20493359228709e-7
+HMDB02523 -0.0457401508672373 1.59320308480663e-8 1.20493359228709e-7
+HMDB03407 -0.0457401508672373 1.59320308480663e-8 1.20493359228709e-7
+HMDB10720 -0.0457401508672373 1.59320308480663e-8 1.20493359228709e-7
+HMDB31209 -0.0457401508672373 1.59320308480663e-8 1.20493359228709e-7
+HMDB33977 -0.0457401508672373 1.59320308480663e-8 1.20493359228709e-7
+HMDB34439 -0.0457401508672373 1.59320308480663e-8 1.20493359228709e-7
+HMDB03609 -0.0414586189510491 6.9920791484094e-9 5.49147139271231e-8
+HMDB39426 -0.0414586189510491 6.9920791484094e-9 5.49147139271231e-8
+HMDB00039 0.022048220035904 0.00188217842601743 0.00492744659734308
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+HMDB40579 0.022048220035904 0.00188217842601743 0.00492744659734308
+HMDB00056 -0.0470472624456466 2.67434311374736e-15 6.50120075984776e-14
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+HMDB00271 -0.0470472624456466 2.67434311374736e-15 6.50120075984776e-14
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+HMDB00190 -0.0695715477529593 2.67123071143295e-10 2.75487530946772e-9
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+HMDB30299 0.0195366564532709 0.119246887554601 0.18117719076376201
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+HMDB00228 0.00917355977870749 0.0381720614329369 0.0700965372716341
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+HMDB31339 -0.0133505305961492 0.0587016998067956 0.0998907258378971
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+HMDB40271 -0.0108506662834333 0.00934719749869359 0.0206569018315285
+HMDB30276 -0.031225981563022 1.67826635990664e-8 1.25993378931227e-7
+HMDB11749 -0.0272481930758275 2.17769482452712e-4 7.1723432769103e-4
+HMDB34587 -0.0272481930758275 2.17769482452712e-4 7.1723432769103e-4
+HMDB40518 -0.0272481930758275 2.17769482452712e-4 7.1723432769103e-4
+HMDB60309 -0.0272481930758275 2.17769482452712e-4 7.1723432769103e-4
+HMDB29387 -0.0211179966101973 1.75640342659495e-4 5.9380393991836e-4
+HMDB29615 -0.0211179966101973 1.75640342659495e-4 5.9380393991836e-4
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+HMDB38394 -0.0225978922570587 2.54434124766176e-7 1.60356321843374e-6
+HMDB41945 -0.0225978922570587 2.54434124766176e-7 1.60356321843374e-6
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+HMDB31716 0.059192142356526 9.64758523436075e-7 5.38261449414335e-6
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+HMDB41475 0.059192142356526 9.64758523436075e-7 5.38261449414335e-6
+HMDB01858 0.00355119729074538 0.401079194835486 0.483473267918573
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+HMDB02055 0.00355119729074538 0.401079194835486 0.483473267918573
+HMDB03119 0.00355119729074538 0.401079194835486 0.483473267918573
+HMDB33895 0.00355119729074538 0.401079194835486 0.483473267918573
+HMDB00965 -0.132951980997225 9.20378526297991e-16 2.68487564385785e-14
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+HMDB01206 -0.060718229679436 4.16703160559548e-12 5.90908231849026e-11
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+HMDB10659 0.0221751225179307 1.06744843393293e-5 4.80116674469395e-5
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+HMDB09937 -0.0276875215355812 2.21671372744719e-7 1.41454044732724e-6
+HMDB09938 -0.0276875215355812 2.21671372744719e-7 1.41454044732724e-6
+HMDB09945 -0.0276875215355812 2.21671372744719e-7 1.41454044732724e-6
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+HMDB09980 -0.0276875215355812 2.21671372744719e-7 1.41454044732724e-6
+HMDB09981 -0.0276875215355812 2.21671372744719e-7 1.41454044732724e-6
+HMDB09991 -0.0276875215355812 2.21671372744719e-7 1.41454044732724e-6
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+HMDB10014 -0.0276875215355812 2.21671372744719e-7 1.41454044732724e-6
+HMDB10017 -0.0276875215355812 2.21671372744719e-7 1.41454044732724e-6
+HMDB10018 -0.0276875215355812 2.21671372744719e-7 1.41454044732724e-6
+HMDB10021 -0.0276875215355812 2.21671372744719e-7 1.41454044732724e-6
+HMDB10022 -0.0276875215355812 2.21671372744719e-7 1.41454044732724e-6
+HMDB10024 -0.0276875215355812 2.21671372744719e-7 1.41454044732724e-6
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+HMDB10030 -0.0276875215355812 2.21671372744719e-7 1.41454044732724e-6
diff -r 000000000000 -r 28e29a3d0eda test-data/proteome.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/proteome.tsv Wed Jun 07 19:48:50 2023 +0000
@@ -0,0 +1,8276 @@
+Symbol logFC pValue adj.pValue
+IFRD1 2.17100926892448 1.51976984734139e-11 1.257609548675e-7
+FAM129A 1.96701389667949 7.79364076028412e-11 3.22461886456755e-7
+FDFT1 -1.7770896907038 2.49353452977254e-10 6.87799941128926e-7
+ASNS 1.45723078606236 4.70888436048425e-10 9.7415045207518e-7
+CTH 1.57397487228467 1.21773665242265e-9 1.66542814540689e-6
+PCK2 1.38119169411237 1.23327992687474e-9 1.66542814540689e-6
+SPINK6 -1.30950487130349 1.40882139188498e-9 1.66542814540689e-6
+ATF4 3.50982732240442 1.89605895623752e-9 1.79559895382218e-6
+SCARA3 -1.35022041391619 1.95291729116612e-9 1.79559895382218e-6
+PRELID1 1.44681897472319 2.19647632502257e-9 1.81758415895618e-6
+SESN2 1.40215149710929 2.56825592512607e-9 1.93202888912893e-6
+PSAT1 1.22666337268055 2.96854058366878e-9 2.0470561108216e-6
+SLMO2 2.15471474123484 3.57482550112632e-9 2.27551392475541e-6
+CHAC1 3.57230210752529 4.94689952350276e-9 2.9239709683561e-6
+DNAJC15 1.4313930499059 5.91930605427288e-9 3.26548383994054e-6
+LARP6 1.76458615305975 6.58642749384814e-9 3.40641796947459e-6
+ALDH1L2 1.09516237195553 7.91070290365098e-9 3.85065097221834e-6
+F5 1.09557894825809 9.42615847700888e-9 4.22324446680393e-6
+VLDLR 1.14563123317803 9.76076013343628e-9 4.22324446680393e-6
+S100P 1.21287828850121 1.02072373820034e-8 4.22324446680393e-6
+NDUFA4 0.901854788617407 1.1904017796326e-8 4.69074986974274e-6
+WISP2 -0.993062607111456 2.16210505895252e-8 8.13246334674188e-6
+SELRC1 -1.10098823156136 2.45366119128447e-8 8.82784624255607e-6
+IGSF10 -0.905016516619793 3.21855619295394e-8 1.10973135402891e-5
+PCSK9 -0.834891541905324 3.48344364644565e-8 1.11763573619729e-5
+LRP11 -0.812040726994158 3.52796925420361e-8 1.11763573619729e-5
+ZBED3 0.943862446432877 3.64666645043223e-8 1.11763573619729e-5
+ERRFI1 1.493950826499 4.21470158231139e-8 1.24244607352016e-5
+FADS2 -1.36361055210062 4.46099823900214e-8 1.24244607352016e-5
+SLC38A1 0.949386153607275 4.63505986930124e-8 1.24244607352016e-5
+HLA-E -0.921035702220436 4.79690789022445e-8 1.24244607352016e-5
+ASS1 1.12776264553814 4.80462529941331e-8 1.24244607352016e-5
+SLFN5 0.854171984801411 4.95697225042753e-8 1.24299834461478e-5
+ENDOG -1.42944384145033 5.62704244985018e-8 1.36952283154442e-5
+KIAA0101 -1.24953889526426 7.51760524413393e-8 1.77737666843452e-5
+CARS 0.749743079827229 7.94671502251835e-8 1.82664074475943e-5
+COL3A1 -1.08930102089798 9.11131356721579e-8 2.03773296672191e-5
+FADS1 -0.851637141282293 9.59890058723393e-8 2.0902869041937e-5
+KIF20A -0.8239940106982 1.07361223301614e-7 2.27798493030989e-5
+AURKB -0.786342200164165 1.39090783817318e-7 2.87744059022077e-5
+GARS 0.780915946887437 1.46120306056762e-7 2.94913544541393e-5
+ZWINT -0.721972049412463 1.63524530161956e-7 3.22182258830996e-5
+NUSAP1 -0.801238442057822 1.98520293623894e-7 3.82036146450634e-5
+PTP4A1 0.634990448192124 2.30121849943951e-7 4.32785979155953e-5
+ZNF253 -0.774845788539344 2.42247981084196e-7 4.45467120771493e-5
+TOB1 -0.737114463822263 2.54823131675311e-7 4.53128464261297e-5
+SLC6A9 0.787820766353276 2.57366015955057e-7 4.53128464261297e-5
+ITM2B -0.839609308984228 2.68372197225731e-7 4.62662485842275e-5
+RND3 0.8556948838532 2.76036245914838e-7 4.6616325202965e-5
+NDUFA13 1.00419559171851 2.89061366364607e-7 4.78396561333425e-5
+CKS2 -0.809221719425347 3.17418132673067e-7 4.98548993635427e-5
+KIAA1161 -0.614589608269639 3.20509863104787e-7 4.98548993635427e-5
+CXXC5 -0.751561608205061 3.22380337469782e-7 4.98548993635427e-5
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+LRRC8D -0.00269067696984671 0.94937498229905 0.963699457620785
+STK39 0.00356231604580692 0.949852212531435 0.96404902660242
+SUPT6H 0.00351520851861853 0.94995235805633 0.96404902660242
+NCBP2 -0.00483082707023375 0.951050727882108 0.964969755178516
+PLCB1 -0.00401307444455679 0.951092848729423 0.964969755178516
+BZW2 -0.00476133416155644 0.951236153943238 0.964996833870331
+TYMS -0.00237420148929246 0.951635246797743 0.965283362006781
+TM9SF4 -0.00304831909091963 0.951754670852671 0.965286174936371
+SNAPC3 -0.00369620209354782 0.952113231310254 0.965529935487342
+RPS25 0.00343810092993557 0.952228375046791 0.965529935487342
+PRKCDBP -0.00299706878016526 0.952346452519435 0.965531351947847
+PDIA5 -0.00359418033478232 0.952544436973973 0.965613771402625
+ANKS6 0.00747570432200284 0.953393273212298 0.966355871610946
+DHX15 -0.00217499741149396 0.953742246323882 0.966591192691993
+LYRM4 -0.00377321416531995 0.953973856631289 0.966707526772461
+RAD50 -0.00242485524032254 0.954186803304249 0.966804921922697
+ZNF346 0.00320246685306191 0.954356594981402 0.966858572902927
+MTO1 -0.00410551163217932 0.954811295806328 0.967200816843844
+SRP19 0.0066904742608962 0.954945857234926 0.967218723209181
+TBC1D5 0.00205844308509118 0.955294437437387 0.967453367983647
+SRC -0.00546716128600266 0.955717511043748 0.967763387651372
+ZNF654 -0.00516597165361343 0.956133925380827 0.968066589077002
+TAOK1 -0.00290103132144548 0.956654387427726 0.968388323734294
+DYNLT3 -0.00548530071609221 0.956716408222491 0.968388323734294
+LSM11 0.00514036673607698 0.956802771583273 0.968388323734294
+KIAA0196 -0.00265078124084095 0.957133774341679 0.968487206934557
+SPRTN 0.00657189965669325 0.957134547227892 0.968487206934557
+MOSPD2 -0.00225653954014682 0.957315137061422 0.968551504974112
+CSNK1G2 0.0129949643018588 0.958230989951689 0.969359589468243
+RFX3 -0.00309366688733448 0.958458203854734 0.969470924935574
+DDX59 0.00279615954999901 0.958682935693593 0.969579722911816
+MPND -0.00345531510631503 0.958855798587518 0.969636042198669
+TRAM2 0.00686484999551329 0.959449626041047 0.970117993095022
+ASCC1 0.002164301479473 0.95967619170541 0.97022852612856
+ATP6V1F -0.00419228721998621 0.959924984196426 0.970361500638337
+FIBP -0.00334058902573986 0.960556307184242 0.970881084884524
+HS1BP3 0.00406775924349922 0.960978974644346 0.971189669660718
+PAPOLA 0.00268707630239984 0.961544590414507 0.971642628609115
+MYH9 0.00452883192766773 0.96274112142997 0.972732940150549
+RIPK1 -0.00284309162779461 0.963228022559219 0.973106078217255
+PPP3CA -0.00319671530806431 0.963364623017989 0.973125275326399
+FBXL19 -0.00349274654123466 0.964216756731171 0.973774537988059
+AP1S2 -0.00335616310578413 0.964242726800502 0.973774537988059
+CDC42BPB 0.0023782574748239 0.964730727003393 0.974148476626367
+TRIM7 0.00274082585795732 0.96502703822746 0.974328787375822
+TMEM120A 0.00407847598831257 0.965535918530074 0.974723645948074
+SYBU -0.00350040292143117 0.966068644648705 0.975142477978535
+SRSF1 -0.00228015773359225 0.966716136296009 0.97567703718130006
+MBTPS2 -0.00354104380588627 0.967044475107485 0.975889394087127
+C12orf23 -0.00287027664180606 0.967182025636721 0.975909189384693
+CFL1 0.0039210610216064996 0.968050373667712 0.976666281650855
+EXOSC4 -0.00222006729936375 0.968452845420829 0.976953223925072
+PIK3C2B -0.0041849367864879 0.969562454882566 0.977953353748566
+YTHDC1 0.00220885031165086 0.969721086649207 0.977994148936281
+MPP5 -0.00126691663994993 0.97030044524602 0.978459198685208
+FIP1L1_1 -0.0103257158912209 0.97059983132110506 0.978641842839301
+MIEF1 -0.00146377886703242 0.971428634387112 0.979358180988469
+NDEL1 0.00213972947626218 0.971757214720337 0.979521782871646
+MYO1C -0.00166916760927549 0.971827654063591 0.979521782871646
+CASP9 0.00186201421181131 0.972792503342167 0.980374858745151
+CISD1 0.00129134277062803 0.973244279847791 0.980710717942094
+NT5C3A 0.0011852953169722 0.973508123601874 0.98082166127167
+POLR2B 0.00111180683375789 0.973688520027536 0.98082166127167
+ITPRIPL2 0.00273789722934747 0.973771787713174 0.98082166127167
+STRA13 0.00280260282851064 0.973828491723026 0.98082166127167
+EXOC4 -0.00121639189234113 0.97428561420282 0.981162645433654
+HMGN2 0.00438816583687451 0.974689589843927 0.981349602991315
+BUB3 0.00130739815342285 0.974758414039873 0.981349602991315
+POLR3G 0.00467304468681107 0.974827037654213 0.981349602991315
+BCL9 -0.0019075458004103 0.975008122927501 0.981412506656741
+RPL24 -0.00213055857754529 0.975967509165797 0.982249265840489
+SIRT1 0.00172703006692387 0.976076823324029 0.982249265840489
+CENPC -0.00129888560737967 0.976838959527914 0.982896691402418
+PTGS1 0.00283268290649463 0.978988414531366 0.984939711884141
+KDM3A -0.00148481322038485 0.979460667411376 0.985295042891944
+RAB10 0.00128673849019556 0.979867388020873 0.985584372902969
+OS9 -0.00186938532455549 0.98037798441374 0.985870776211496
+SH3PXD2A -0.00203725639538899 0.980390406941921 0.985870776211496
+CRTC3 -0.00150860489831661 0.980790399901103 0.986153166364718
+SRGAP1 0.00141168161596283 0.981644861158653 0.98689238562603
+UCK1 -0.00207958379289508 0.981901194990124 0.987030173535383
+CADM4 0.00177779132718836 0.98230616872059 0.987197539151131
+CKMT1A -8.24257128518191e-4 0.982457662860829 0.987197539151131
+HEXA 8.28900607565686e-4 0.982475711945914 0.987197539151131
+KLHDC10 -0.00341741615570612 0.982544886096521 0.987197539151131
+HIP1R -9.96352489925911e-4 0.982833167881795 0.987301892689877
+VBP1 -0.00102813244280853 0.982887370631929 0.987301892689877
+PLCL2 -0.00197352140785245 0.983300754292166 0.987597249880771
+ANXA6 -9.63957809009486e-4 0.983750862718863 0.987929416140606
+ACTR1A -0.00142398778348962 0.983992468872903 0.988052139294172
+SIRPA -0.0011483141202166501 0.984319531238841 0.988260631036327
+CEP85L 0.0011241719714441 0.984618757147316 0.988441127671241
+GEMIN4 8.85391638851374e-4 0.985282861225476 0.988987830742457
+TRAPPC6B 0.00127697257047288 0.985429266561242 0.989014818774321
+C1orf198 0.00181331241736693 0.985800026473636 0.989266943859973
+FAM188B -0.00290305790297918 0.986842246699505 0.990192747840234
+KAL1 -0.00468633242773997 0.98701951895038 0.990250547928516
+MIER3 0.00298353305365939 0.987369056492619 0.990312922998574
+HN1 -0.00142430503294744 0.987412980075915 0.990312922998574
+HSPB8 7.76206291130954e-4 0.987440716333684 0.990312922998574
+SRP14 0.0010232057036319 0.987681326555633 0.990434195013071
+PRPS1 -6.45398851954582e-4 0.988580959526359 0.991216217142932
+CSNK2B 4.81976873256684e-4 0.989123670891745 0.991640220090767
+USP32 -5.08633248005097e-4 0.98958692310659 0.991984468650155
+GEMIN7 -0.00125412327971297 0.989962197266786 0.992240453292473
+RIPK2 -6.27242303687048e-4 0.990514276757734 0.992673566691322
+SLC9A6 -7.59651130186612e-4 0.990767405389334 0.992807008912174
+GUSB -7.2436835249956e-4 0.991577578344927 0.993498542293773
+SEH1L 5.4658008260855e-4 0.991948490806523 0.993749850051329
+PWWP2B 0.00121275638794849 0.992627852111002 0.994310068541162
+AP5B1 -4.32669290459486e-4 0.993432924620357 0.994996060425255
+ARNTL 3.16052536415867e-4 0.993732102100046 0.995115782519309
+THAP11 0.00103464439352674 0.99379296999874 0.995115782519309
+REXO1 0.00125420672958132 0.994464514478296 0.995667738331264
+TTC21A -7.81532977215171e-4 0.995387384769103 0.996471160048914
+TPM3 -4.02905617320926e-4 0.995744658186035 0.996630443760696
+PPP1R13B 5.1600456486689e-4 0.995787372690445 0.996630443760696
+MICAL2 2.76393643596329e-4 0.995997543876262 0.996720241332213
+FN1 -2.58494133370313e-4 0.99689891635036 0.997434357481888
+ZBTB5 -1.37914580930598e-4 0.996952213985824 0.997434357481888
+COPA 1.05578131729622e-4 0.998444512763599 0.998806617881865
+AKTIP 1.50880700191536e-4 0.999454954517943 0.999696573025018
+XRCC1 -1.2372981342601e-5 0.999772026690978 0.999859015825647
+SUPT4H1 -3.05334106771582e-5 0.999859015825647 0.999859015825647
diff -r 000000000000 -r 28e29a3d0eda test-data/transcriptome.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/transcriptome.tsv Wed Jun 07 19:48:50 2023 +0000
@@ -0,0 +1,15175 @@
+Symbol logFC pValue adj.pValue
+STC2 0.704500282226347 3.71089306872736e-14 5.63090914248689e-10
+ASNS 0.627966319665099 2.0255326292911e-13 1.53677160584316e-9
+PCK2 0.619355311651102 7.77477603404156e-13 3.93248171801822e-9
+FAM129A 0.880826438814874 1.06943563433091e-12 4.05690407883431e-9
+NUPR1 0.588841194242637 1.54636710326692e-12 4.69291488499446e-9
+ASS1 0.624138659380686 2.41695823247016e-12 6.11248736991704e-9
+TRIB3 0.86297487467659 3.46130939111073e-12 7.50312981438775e-9
+PSAT1 0.469619454647728 1.41593552178526e-11 2.68567570094618e-8
+FADS2 -0.397872623139451 2.00851788591982e-11 3.38636115566082e-8
+BMF -0.590480389664462 3.8446423466847e-11 5.83386029685936e-8
+SESN2 0.609514732887674 4.78507080806277e-11 6.60078767650405e-8
+GDF15 0.936936029787823 5.45997234968492e-11 6.90413503617659e-8
+WARS 0.335627820987674 7.4570266737941e-11 8.70407098062705e-8
+SLC6A9 0.406200205524983 1.12457110729216e-10 1.21887442728937e-7
+CHAC1 1.45474233419102 1.46636951721807e-10 1.4833794036178e-7
+VEGFA 0.381554890128001 1.8661105799545e-10 1.72246954436364e-7
+GPT2 0.515468087344662 1.92974708410319e-10 1.72246954436364e-7
+MARS 0.309316030617479 2.2575158143115e-10 1.90308583146459e-7
+CARS 0.375811955851783 2.74959554544042e-10 2.11962735044355e-7
+MTHFD2 0.468336628805509 2.79376215954072e-10 2.11962735044355e-7
+INSIG1 -0.508872341985173 3.51468457261962e-10 2.53961065261572e-7
+LARP6 0.651200265452626 3.9000696993804e-10 2.57390487303515e-7
+EIF4EBP1 0.39781539983742 3.90139792275e-10 2.57390487303515e-7
+SARS 0.28266275512208 4.92761973719958e-10 3.09233070885333e-7
+IDH1 0.291986761085429 5.09478500865515e-10 3.09233070885333e-7
+CEBPG 0.425667840930084 5.66385614668879e-10 3.30551358345599e-7
+PSPH 0.435623588643199 5.92600427114492e-10 3.33041440038345e-7
+ASF1B -0.362870511536212 6.394431595813e-10 3.46532517981666e-7
+UNC5B 1.6816745643023 7.72770722162363e-10 4.04345618554886e-7
+AJUBA 0.443379616186069 8.75626472578165e-10 4.42891869830036e-7
+GARS 0.324448707903362 1.00110053900395e-9 4.90022567059547e-7
+SLC1A5 0.257571321924166 1.31058087788177e-9 6.06702929384363e-7
+C6orf48 0.349759534720501 1.31944092985923e-9 6.06702929384363e-7
+BCAT1 0.457197936829043 1.84698044952342e-9 8.24296510031423e-7
+AMIGO2 0.416562600697803 2.37222347980217e-9 1.00004628327156e-6
+CDKN2C -0.282700228263487 2.37258904690762e-9 1.00004628327156e-6
+ATF3 0.671925395165331 2.50411962501266e-9 1.02695976189033e-6
+MEOX1 -0.68834135622312 2.80771464561384e-9 1.10557404664781e-6
+CTH 0.869872912460933 2.84153076441706e-9 1.10557404664781e-6
+ALDH1L2 0.7713556268181 3.4046575828848e-9 1.29155685406735e-6
+S100P 1.12974082445842 3.97201032560321e-9 1.47003133367569e-6
+FDFT1 -0.294031210384657 4.8822183870755e-9 1.76387575727342e-6
+KRT19 -0.424151176401533 6.42997143542185e-9 2.26903224560677e-6
+IARS 0.20763052159502501 7.69697064653723e-9 2.63303671383474e-6
+IL20RB 0.733295193003586 7.80853117981833e-9 2.63303671383474e-6
+SCD -0.217792840011739 8.19842770455638e-9 2.70441178236823e-6
+IGSF10 -0.20716826969625 9.46637151933383e-9 3.05622811562493e-6
+GADD45A 0.539934056770522 1.06221034982652e-8 3.35791246838907e-6
+XPOT 0.268979736455839 1.13306810802815e-8 3.50881132065698e-6
+AARS 0.222853251872265 1.19344915903575e-8 3.58463419823735e-6
+YARS 0.215534347928307 1.20479994800386e-8 3.58463419823735e-6
+ERRFI1 0.421169493373689 1.24880776104427e-8 3.64411710886264e-6
+RRM2 -0.317872011771425 1.50347425878583e-8 4.28813234604051e-6
+IDI1 -0.411509181300695 1.52602574592189e-8 4.28813234604051e-6
+ASS1P9 1.15397931088342 1.58030820588866e-8 4.35992667566447e-6
+VLDLR 0.672932216314967 1.6698977162507e-8 4.45630020021719e-6
+CLGN 0.404117751484052 1.69384994276749e-8 4.45630020021719e-6
+RGCC -0.453512271811646 1.71237430572711e-8 4.45630020021719e-6
+SHMT2 0.235611237430561 1.74124966656655e-8 4.45630020021719e-6
+PLCXD3 -0.463524617673655 1.7620799526363e-8 4.45630020021719e-6
+GAS5 0.247672757375438 1.89946395806483e-8 4.7249944425698e-6
+LGR4 -0.28645249491221 1.93757021218831e-8 4.74014607937185e-6
+SLC1A4 0.267633805381842 1.96803218004763e-8 4.74014607937185e-6
+LONP1 0.241835246978595 2.01391964713265e-8 4.77487761337357e-6
+S100A4 -0.237850711251943 2.14786253473932e-8 5.01410247725145e-6
+PHGDH 0.229947526233384 2.28739361874053e-8 5.25892587435891e-6
+MAP1A -0.521181751998103 2.33716899660934e-8 5.27915478291686e-6
+RP11-382M14.1 1.27658128760577 2.3955760049532e-8 5.27915478291686e-6
+ADM2 1.25497133135791 2.40056465019944e-8 5.27915478291686e-6
+ASS1P12 1.13275095205903 2.58397198936279e-8 5.60131299522728e-6
+TUBA1A -0.280369608550124 2.64766461233519e-8 5.65854406022171e-6
+TIMP4 0.583418059325131 2.74791377565825e-8 5.70382329043418e-6
+PPP1R15A 0.572422339238252 2.77757100929054e-8 5.70382329043418e-6
+PRKCB -0.478369037935187 2.78161937190015e-8 5.70382329043418e-6
+PSAT1P3 0.794660352923572 2.9611166569063e-8 5.99093122025282e-6
+ATF4 0.183973975082908 3.08966416300889e-8 6.09735620013072e-6
+ASS1P11 1.22103280295456 3.13231732937496e-8 6.09735620013072e-6
+DDIT3 0.857426072047891 3.14055342485103e-8 6.09735620013072e-6
+TCEA1P2 0.402829917319312 3.1747634257474e-8 6.09735620013072e-6
+KCTD15 0.270888100570315 3.21463355746973e-8 6.09735620013072e-6
+SLC7A11 0.274013428607222 3.37505130599036e-8 6.32259611322195e-6
+ETV5 1.24125642334775 3.74728252919992e-8 6.93430062171703e-6
+DHCR24 -0.196394384351996 4.28396294245522e-8 7.83191008298982e-6
+AKAP12 -0.241504185052597 4.34385031337442e-8 7.84685531608851e-6
+CBS 0.223518971310903 4.54626083419868e-8 8.11587787036832e-6
+FADS1 -0.181398069631374 4.67186760315064e-8 8.24313011746602e-6
+PALMD -0.335422179715229 4.8430947785682e-8 8.44702530689585e-6
+METTL7A -0.660763679550601 5.00416257329574e-8 8.6287685099079e-6
+UHRF1BP1 0.301784045643583 5.14531225954488e-8 8.77246834003753e-6
+EPRS 0.180717003244521 5.21262081126456e-8 8.78847868779205e-6
+DHCR7 -0.243108592678477 5.43418348057573e-8 9.06135166310508e-6
+ULBP1 0.878381656201259 5.5318184747998e-8 9.12389277571871e-6
+CDC42EP1 0.291834115886416 5.6401287016877e-8 9.20250676552787e-6
+STARD4 -0.479745913595582 5.98569862799396e-8 9.66244584906174e-6
+QPRT -0.442453863035968 6.1505864783656e-8 9.77502855901452e-6
+CRYAB -0.420477203573589 6.18428062254774e-8 9.77502855901452e-6
+BEX2 2.2399949318556 6.27127426814287e-8 9.81034182936081e-6
+GRB10 0.216180154702368 6.37354260891059e-8 9.86858525996013e-6
+CLDN1 0.34223259718068 6.48727027864849e-8 9.9432160816376e-6
+TRIM25 0.237898862975995 6.75539522633762e-8 1.02506367164447e-5
+COL3A1 -0.182417083501265 7.09045953844812e-8 1.05483003180216e-5
+PID1 0.429995016123683 7.09059333358512e-8 1.05483003180216e-5
+SERPINE2 0.23917868193634 7.36418786521733e-8 1.07805739474048e-5
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