Nothing
R/GSCstatBatch.R
In piano: Platform for integrative analysis of omics data
Defines functions
GSCstatBatch
GSCstatBatch <- function(statistics, statType, gsc, method, signMethod, gseaParam, signs, nPerm) {
# Create result list object:
res <- list()
res$statsAll <- vector()
res$statsAllTestUp <- vector()
res$statsAllTestDn <- vector()
res$statsAbs <- vector()
res$statsUp <- vector()
res$statsDn <- vector()
res$nGenes <- vector()
res$nGenesUp <- vector()
res$nGenesDn <- vector()
res$pValuesAll <- vector()
res$pValuesAllUp <- vector()
res$pValuesAllDn <- vector()
res$pValuesAbs <- vector()
res$pValuesUp <- vector()
res$pValuesDn <- vector()
iContrast <- 1 # Remnant from when multiple contrast were allowed
# Preallocate:
gsStatsAll <- rep(NA,length(gsc))
gsStatsAllTestUp <- rep(NA,length(gsc))
gsStatsAllTestDn <- rep(NA,length(gsc))
gsStatsAbs <- rep(NA,length(gsc))
gsStatsUp <- rep(NA,length(gsc))
gsStatsDn <- rep(NA,length(gsc))
nGenes <- rep(0,length(gsc))
nGenesUp <- rep(0,length(gsc))
nGenesDn <- rep(0,length(gsc))
pValuesAll <- rep(NA,length(gsc))
pValuesAllUp <- rep(NA,length(gsc))
pValuesAllDn <- rep(NA,length(gsc))
pValuesAbs <- rep(NA,length(gsc))
pValuesUp <- rep(NA,length(gsc))
pValuesDn <- rep(NA,length(gsc))
# Get statistics for current contrast:
statsContrast <- statistics[,iContrast]
if(statType %in% c("p-signed","F-signed")) {
signsContrast <- signs[,iContrast]
}
if(statType == "t") {
signsContrast <- sign(statsContrast)
}
# If possible, calculate "directional p-values":
if(method %in% c("stouffer","reporter","tailStrength","wilcoxon","wilcoxon_fast","mean","median","sum") & statType == "p-signed") {
statsContrastTestUp <- abs(statsContrast)
statsContrastTestUp[signsContrast > 0] <- statsContrastTestUp[signsContrast > 0]/2
statsContrastTestUp[signsContrast < 0] <- 1 - statsContrastTestUp[signsContrast < 0]/2
statsContrastTestUp[signsContrast == 0] <- NA
statsContrastTestDn <- 1 - statsContrastTestUp
# Fix zeros and ones in directional p-values:
statsContrastTestUp[statsContrastTestUp < 1e-100] <- 1e-100
statsContrastTestUp[statsContrastTestUp > 0.9999999999999999] <- 0.9999999999999999
statsContrastTestDn[statsContrastTestDn < 1e-100] <- 1e-100
statsContrastTestDn[statsContrastTestDn > 0.9999999999999999] <- 0.9999999999999999
}
# Loop through the gene-sets and calculate gene-set statistics (except from FGSEA which does its own looping, further down):
for(iGeneSet in 1:length(gsc)) {
#************************
# Fisher:
#************************
if(method == "fisher") {
# Get statistics for gene-set:
indGenesInSet <- names(statsContrast) %in% gsc[[iGeneSet]]
statsGenesInSet <- statsContrast[indGenesInSet]
nGenes[iGeneSet] <- length(statsGenesInSet)
if(nGenes[iGeneSet] > 0) {
# Genes up/dn (partly redundant code added later as a fix):
if(exists("signsContrast")) {
nGenesUp[iGeneSet] <- sum(signsContrast[indGenesInSet]>0)
nGenesDn[iGeneSet] <- sum(signsContrast[indGenesInSet]<0)
}
# "Mixed" gene-set statistic:
gsStatsAbs[iGeneSet] <- calcGeneSetStat(abs(statsGenesInSet), method)
# "Subset-up" gene-set statistic:
if(statType == "p-signed" & signMethod != "sampleperm") {
signsGenesInSet <- signsContrast[indGenesInSet]
sel <- statsGenesInSet[signsGenesInSet > 0]
nGenesUp[iGeneSet] <- length(sel)
if(nGenesUp[iGeneSet] > 0) {
gsStatsUp[iGeneSet] <- calcGeneSetStat(sel, method)
}
# "Subset-dn" gene-set statistic:
sel <- abs(statsGenesInSet[signsGenesInSet < 0])
nGenesDn[iGeneSet] <- length(sel)
if(nGenesDn[iGeneSet] > 0) {
gsStatsDn[iGeneSet] <- calcGeneSetStat(sel, method)
}
}
}
#************************
# Stouffer:
# Reporter:
# Tail strength:
#************************
} else if(method %in% c("stouffer","reporter","tailStrength")) {
# Get statistics for gene-set:
indGenesInSet <- names(statsContrast) %in% gsc[[iGeneSet]]
statsGenesInSet <- statsContrast[indGenesInSet]
nGenes[iGeneSet] <- length(statsGenesInSet)
if(nGenes[iGeneSet] > 0) {
# Genes up/dn (partly redundant code added later as a fix):
if(exists("signsContrast")) {
nGenesUp[iGeneSet] <- sum(signsContrast[indGenesInSet]>0)
nGenesDn[iGeneSet] <- sum(signsContrast[indGenesInSet]<0)
}
# "Directional" gene-set statistics:
if(statType == "p-signed") {
statsGenesInSetTestUp <- statsContrastTestUp[indGenesInSet]
statsGenesInSetTestDn <- statsContrastTestDn[indGenesInSet]
statsGenesInSetTestUp <- statsGenesInSetTestUp[!is.na(statsGenesInSetTestUp)]
statsGenesInSetTestDn <- statsGenesInSetTestDn[!is.na(statsGenesInSetTestDn)]
gsStatsAllTestUp[iGeneSet] <- calcGeneSetStat(statsGenesInSetTestUp, method)
gsStatsAllTestDn[iGeneSet] <- calcGeneSetStat(statsGenesInSetTestDn, method)
}
# "Mixed" gene-set statistic:
gsStatsAbs[iGeneSet] <- calcGeneSetStat(abs(statsGenesInSet), method)
# "Subset-up" gene-set statistic:
if(statType == "p-signed" & signMethod != "sampleperm") {
signsGenesInSet <- signsContrast[indGenesInSet]
sel <- statsGenesInSet[signsGenesInSet > 0]
nGenesUp[iGeneSet] <- length(sel)
if(nGenesUp[iGeneSet] > 0) {
gsStatsUp[iGeneSet] <- calcGeneSetStat(sel, method)
}
# "Subset-dn" gene-set statistic:
sel <- abs(statsGenesInSet[signsGenesInSet < 0])
nGenesDn[iGeneSet] <- length(sel)
if(nGenesDn[iGeneSet] > 0) {
gsStatsDn[iGeneSet] <- calcGeneSetStat(sel, method)
}
}
}
#************************
# Wilcoxon:
#************************
} else if(method == "wilcoxon") {
# Get statistics for gene-set:
indGenesInSet <- names(statsContrast) %in% gsc[[iGeneSet]]
statsGenesInSet <- statsContrast[indGenesInSet]
statsNotInSet <- statsContrast[!indGenesInSet]
if(statType %in% c("p-signed","F-signed")) {
signsGenesInSet <- signsContrast[indGenesInSet]
signsNotInSet <- signsContrast[!indGenesInSet]
}
nGenes[iGeneSet] <- length(statsGenesInSet)
if(nGenes[iGeneSet] > 0) {
# Genes up/dn (partly redundant code added later as a fix):
if(exists("signsContrast")) {
nGenesUp[iGeneSet] <- sum(signsContrast[indGenesInSet]>0)
nGenesDn[iGeneSet] <- sum(signsContrast[indGenesInSet]<0)
}
# "Directional" gene-set statistics:
if(statType == "p-signed") {
statsGenesInSetTestUp <- statsContrastTestUp[indGenesInSet]
statsGenesInSetTestDn <- statsContrastTestDn[indGenesInSet]
statsGenesInSetTestUp <- statsGenesInSetTestUp[!is.na(statsGenesInSetTestUp)]
statsGenesInSetTestDn <- statsGenesInSetTestDn[!is.na(statsGenesInSetTestDn)]
statsNotInSetTestUp <- statsContrastTestUp[!indGenesInSet]
statsNotInSetTestDn <- statsContrastTestDn[!indGenesInSet]
statsNotInSetTestUp <- statsNotInSetTestUp[!is.na(statsNotInSetTestUp)]
statsNotInSetTestDn <- statsNotInSetTestDn[!is.na(statsNotInSetTestDn)]
tmp <- calcGeneSetStat(statsGenesInSetTestUp, "wilcoxon_less", statsNotInSetTestUp)
gsStatsAllTestUp[iGeneSet] <- tmp[1]
pValuesAllUp[iGeneSet] <- tmp[2]
tmp <- calcGeneSetStat(statsGenesInSetTestDn, "wilcoxon_less", statsNotInSetTestDn)
gsStatsAllTestDn[iGeneSet] <- tmp[1]
pValuesAllDn[iGeneSet] <- tmp[2]
} else if(statType == "t") {
tmp <- calcGeneSetStat(statsGenesInSet, "wilcoxon_two.sided", statsNotInSet)
gsStatsAll[iGeneSet] <- tmp[1]
#pValuesAll[iGeneSet] <- tmp[2]
tmp <- calcGeneSetStat(statsGenesInSet, "wilcoxon_greater", statsNotInSet)
pValuesAllUp[iGeneSet] <- tmp[2]
tmp <- calcGeneSetStat(statsGenesInSet, "wilcoxon_less", statsNotInSet)
pValuesAllDn[iGeneSet] <- tmp[2]
}
# "Mixed" gene-set statistic:
if(statType %in% c("p","p-signed")) {
tmp <- calcGeneSetStat(abs(statsGenesInSet), "wilcoxon_less", abs(statsNotInSet))
gsStatsAbs[iGeneSet] <- tmp[1]
pValuesAbs[iGeneSet] <- tmp[2]
} else if(statType %in% c("t","F","F-signed")) {
tmp <- calcGeneSetStat(abs(statsGenesInSet), "wilcoxon_greater", abs(statsNotInSet))
gsStatsAbs[iGeneSet] <- tmp[1]
pValuesAbs[iGeneSet] <- tmp[2]
}
# "Subset-up" gene-set statistic:
if(statType %in% c("t","p-signed","F-signed") & signMethod != "sampleperm") {
if(statType == "t") {
sel <- statsGenesInSet[statsGenesInSet > 0]
} else {
sel <- statsGenesInSet[signsGenesInSet > 0]
}
nGenesUp[iGeneSet] <- length(sel)
if(nGenesUp[iGeneSet] > 0) {
if(statType == "p-signed") {
tmp <- calcGeneSetStat(sel, "wilcoxon_less", statsNotInSet[signsNotInSet > 0])
gsStatsUp[iGeneSet] <- tmp[1]
pValuesUp[iGeneSet] <- tmp[2]
} else if(statType == "t") {
tmp <- calcGeneSetStat(sel, "wilcoxon_greater", statsNotInSet[statsNotInSet > 0])
gsStatsUp[iGeneSet] <- tmp[1]
pValuesUp[iGeneSet] <- tmp[2]
} else if(statType == "F-signed") {
tmp <- calcGeneSetStat(sel, "wilcoxon_greater", statsNotInSet[signsNotInSet > 0])
gsStatsUp[iGeneSet] <- tmp[1]
pValuesUp[iGeneSet] <- tmp[2]
}
}
# "Subset-dn" gene-set statistic:
if(statType == "t") {
sel <- abs(statsGenesInSet[statsGenesInSet < 0])
} else {
sel <- abs(statsGenesInSet[signsGenesInSet < 0])
}
nGenesDn[iGeneSet] <- length(sel)
if(nGenesDn[iGeneSet] > 0) {
if(statType == "p-signed") {
tmp <- calcGeneSetStat(sel, "wilcoxon_less", abs(statsNotInSet[signsNotInSet < 0]))
gsStatsDn[iGeneSet] <- tmp[1]
pValuesDn[iGeneSet] <- tmp[2]
} else if(statType == "t") {
tmp <- calcGeneSetStat(sel, "wilcoxon_greater", abs(statsNotInSet[statsNotInSet < 0]))
gsStatsDn[iGeneSet] <- tmp[1]
pValuesDn[iGeneSet] <- tmp[2]
} else if(statType == "F-signed") {
tmp <- calcGeneSetStat(sel, "wilcoxon_greater", abs(statsNotInSet[signsNotInSet < 0]))
gsStatsDn[iGeneSet] <- tmp[1]
pValuesDn[iGeneSet] <- tmp[2]
}
}
}
}
#************************
# Wilcoxon, fast (only used by GSCstatSamplePerm):
#************************
} else if(method == "wilcoxon_fast") {
# Get statistics for gene-set:
indGenesInSet <- names(statsContrast) %in% gsc[[iGeneSet]]
statsGenesInSet <- statsContrast[indGenesInSet]
statsNotInSet <- statsContrast[!indGenesInSet]
if(statType %in% c("p-signed","F-signed")) {
signsGenesInSet <- signsContrast[indGenesInSet]
signsNotInSet <- signsContrast[!indGenesInSet]
}
nGenes[iGeneSet] <- length(statsGenesInSet)
if(nGenes[iGeneSet] > 0) {
# Genes up/dn (partly redundant code added later as a fix):
if(exists("signsContrast")) {
nGenesUp[iGeneSet] <- sum(signsContrast[indGenesInSet]>0)
nGenesDn[iGeneSet] <- sum(signsContrast[indGenesInSet]<0)
}
# "Directional" gene-set statistics:
if(statType == "p-signed") {
statsGenesInSetTestUp <- statsContrastTestUp[indGenesInSet]
statsGenesInSetTestDn <- statsContrastTestDn[indGenesInSet]
statsGenesInSetTestUp <- statsGenesInSetTestUp[!is.na(statsGenesInSetTestUp)]
statsGenesInSetTestDn <- statsGenesInSetTestDn[!is.na(statsGenesInSetTestDn)]
statsNotInSetTestUp <- statsContrastTestUp[!indGenesInSet]
statsNotInSetTestDn <- statsContrastTestDn[!indGenesInSet]
statsNotInSetTestUp <- statsNotInSetTestUp[!is.na(statsNotInSetTestUp)]
statsNotInSetTestDn <- statsNotInSetTestDn[!is.na(statsNotInSetTestDn)]
gsStatsAllTestUp[iGeneSet] <- calcGeneSetStat(statsGenesInSetTestUp, "wilcoxon_fast", statsNotInSetTestUp)
gsStatsAllTestDn[iGeneSet] <- calcGeneSetStat(statsGenesInSetTestDn, "wilcoxon_fast", statsNotInSetTestDn)
} else if(statType == "t") {
gsStatsAll[iGeneSet] <- calcGeneSetStat(statsGenesInSet, "wilcoxon_fast", statsNotInSet)
}
# "Mixed" gene-set statistic:
if(statType %in% c("p","p-signed")) {
gsStatsAbs[iGeneSet] <- calcGeneSetStat(abs(statsGenesInSet), "wilcoxon_fast", abs(statsNotInSet))
} else if(statType %in% c("t","F","F-signed")) {
gsStatsAbs[iGeneSet] <- calcGeneSetStat(abs(statsGenesInSet), "wilcoxon_fast", abs(statsNotInSet))
}
# "Subset-up" gene-set statistic:
if(statType %in% c("t","p-signed","F-signed") & signMethod != "sampleperm") {
if(statType == "t") {
sel <- statsGenesInSet[statsGenesInSet > 0]
} else {
sel <- statsGenesInSet[signsGenesInSet > 0]
}
nGenesUp[iGeneSet] <- length(sel)
if(nGenesUp[iGeneSet] > 0) {
if(statType == "p-signed") {
gsStatsUp[iGeneSet] <- calcGeneSetStat(sel, "wilcoxon_fast", statsNotInSet[signsNotInSet > 0])
} else if(statType == "t") {
gsStatsUp[iGeneSet] <- calcGeneSetStat(sel, "wilcoxon_fast", statsNotInSet[statsNotInSet > 0])
} else if(statType == "F-signed") {
gsStatsUp[iGeneSet] <- calcGeneSetStat(sel, "wilcoxon_fast", statsNotInSet[signsNotInSet > 0])
}
}
# "Subset-dn" gene-set statistic:
if(statType == "t") {
sel <- abs(statsGenesInSet[statsGenesInSet < 0])
} else {
sel <- abs(statsGenesInSet[signsGenesInSet < 0])
}
nGenesDn[iGeneSet] <- length(sel)
if(nGenesDn[iGeneSet] > 0) {
if(statType == "p-signed") {
gsStatsDn[iGeneSet] <- calcGeneSetStat(sel, "wilcoxon_fast", abs(statsNotInSet[signsNotInSet < 0]))
} else if(statType == "t") {
gsStatsDn[iGeneSet] <- calcGeneSetStat(sel, "wilcoxon_fast", abs(statsNotInSet[statsNotInSet < 0]))
} else if(statType == "F-signed") {
gsStatsDn[iGeneSet] <- calcGeneSetStat(sel, "wilcoxon_fast", abs(statsNotInSet[signsNotInSet < 0]))
}
}
}
}
#************************
# Mean:
# Median:
# Sum:
#************************
} else if(method %in% c("mean","median","sum")) {
# Get statistics for gene-set:
indGenesInSet <- names(statsContrast) %in% gsc[[iGeneSet]]
statsGenesInSet <- statsContrast[indGenesInSet]
if(statType %in% c("p-signed","F-signed")) {
signsGenesInSet <- signsContrast[indGenesInSet]
}
nGenes[iGeneSet] <- length(statsGenesInSet)
if(nGenes[iGeneSet] > 0) {
# Genes up/dn (partly redundant code added later as a fix):
if(exists("signsContrast")) {
nGenesUp[iGeneSet] <- sum(signsContrast[indGenesInSet]>0)
nGenesDn[iGeneSet] <- sum(signsContrast[indGenesInSet]<0)
}
# "Directional" gene-set statistics:
if(statType == "p-signed") {
statsGenesInSetTestUp <- statsContrastTestUp[indGenesInSet]
statsGenesInSetTestDn <- statsContrastTestDn[indGenesInSet]
statsGenesInSetTestUp <- statsGenesInSetTestUp[!is.na(statsGenesInSetTestUp)]
statsGenesInSetTestDn <- statsGenesInSetTestDn[!is.na(statsGenesInSetTestDn)]
gsStatsAllTestUp[iGeneSet] <- calcGeneSetStat(statsGenesInSetTestUp, method)
gsStatsAllTestDn[iGeneSet] <- calcGeneSetStat(statsGenesInSetTestDn, method)
} else if(statType == "t") {
gsStatsAll[iGeneSet] <- calcGeneSetStat(statsGenesInSet, method)
}
# "Mixed" gene-set statistic:
gsStatsAbs[iGeneSet] <- calcGeneSetStat(abs(statsGenesInSet), method)
# "Subset-up" gene-set statistic:
if(statType %in% c("p-signed","t","F-signed") & signMethod != "sampleperm") {
if(statType == "t") {
sel <- statsGenesInSet[statsGenesInSet > 0]
} else {
sel <- statsGenesInSet[signsGenesInSet > 0]
}
nGenesUp[iGeneSet] <- length(sel)
if(nGenesUp[iGeneSet] > 0) {
gsStatsUp[iGeneSet] <- calcGeneSetStat(sel, method)
}
# "Subset-dn" gene-set statistic:
if(statType == "t") {
sel <- abs(statsGenesInSet[statsGenesInSet < 0])
} else {
sel <- abs(statsGenesInSet[signsGenesInSet < 0])
}
nGenesDn[iGeneSet] <- length(sel)
if(nGenesDn[iGeneSet] > 0) {
gsStatsDn[iGeneSet] <- calcGeneSetStat(sel, method)
}
}
}
#************************
# Maxmean:
#************************
} else if(method == "maxmean") {
# Get statistics for gene-set:
indGenesInSet <- names(statsContrast) %in% gsc[[iGeneSet]]
statsGenesInSet <- statsContrast[indGenesInSet]
nGenes[iGeneSet] <- length(statsGenesInSet)
if(nGenes[iGeneSet] > 0) {
# Genes up/dn (partly redundant code added later as a fix):
if(exists("signsContrast")) {
nGenesUp[iGeneSet] <- sum(signsContrast[indGenesInSet]>0)
nGenesDn[iGeneSet] <- sum(signsContrast[indGenesInSet]<0)
}
# "Mixed" gene-set statistic:
gsStatsAbs[iGeneSet] <- calcGeneSetStat(statsGenesInSet, method)
}
#************************
# GSEA:
#************************
} else if(method == "gsea") {
# Get statistics for gene-set:
statsContrastSorted <- sort(statsContrast,decreasing=TRUE)
indGenesInSet <- which(names(statsContrastSorted) %in% gsc[[iGeneSet]])
nGenes[iGeneSet] <- length(indGenesInSet)
if(nGenes[iGeneSet] > 0) {
# Genes up/dn (partly redundant code added later as a fix):
if(exists("signsContrast")) {
#nGenesUp[iGeneSet] <- sum(signsContrast[indGenesInSet]>0)
#nGenesDn[iGeneSet] <- sum(signsContrast[indGenesInSet]<0)
nGenesUp[iGeneSet] <- sum(statsContrastSorted[indGenesInSet]>0)
nGenesDn[iGeneSet] <- sum(statsContrastSorted[indGenesInSet]<0)
}
# "Directional" gene-set statistic:
gsStatsAll[iGeneSet] <- calcGeneSetStat(indGenesInSet, method, statsContrastSorted, gseaParam)
}
#************************
# Page:
#************************
} else if(method == "page") {
# Get statistic for gene-set:
indGenesInSet <- names(statsContrast) %in% gsc[[iGeneSet]]
statsGenesInSet <- statsContrast[indGenesInSet]
nGenes[iGeneSet] <- length(statsGenesInSet)
if(nGenes[iGeneSet] > 0) {
# Genes up/dn (partly redundant code added later as a fix):
if(exists("signsContrast")) {
nGenesUp[iGeneSet] <- sum(signsContrast[indGenesInSet]>0)
nGenesDn[iGeneSet] <- sum(signsContrast[indGenesInSet]<0)
}
# "Directional" gene-set statistics:
gsStatsAll[iGeneSet] <- calcGeneSetStat(statsGenesInSet, method, statsContrast)
}
}
}
#************************
# FGSEA:
#************************
if(method == "fgsea") {
# Run FGSEA using the fgsea package:
tmp <- fgsea(gsc, statsContrast, nperm=nPerm, minSize=1, maxSize=Inf, nproc=0, gseaParam=gseaParam)
# Sort the result table so it matches the original gene-set order:
tmp <- tmp[match(tmp$pathway, names(gsc)),]
# Extract the results:
gsStatsAll <- tmp$ES
pValuesAllUp <- rep(NA, length(tmp$pval))
pValuesAllDn <- pValuesAllUp
pValuesAllUp[gsStatsAll>=0] <- tmp$pval[gsStatsAll>=0]
pValuesAllDn[gsStatsAll<0] <- tmp$pval[gsStatsAll<0]
# Calculate number of genes:
nGenes <- unlist(lapply(gsc, length))
nGenesUp <- unlist(lapply(gsc, function(x) sum(signsContrast[x]>0)))
nGenesDn <- unlist(lapply(gsc, function(x) sum(signsContrast[x]<0)))
}
#--------------------
# Save results:
res$statsAll <- cbind(res$statsAll, gsStatsAll)
res$statsAllTestUp <- cbind(res$statsAllTestUp, gsStatsAllTestUp)
res$statsAllTestDn <- cbind(res$statsAllTestDn, gsStatsAllTestDn)
res$statsAbs <- cbind(res$statsAbs, gsStatsAbs)
res$statsUp <- cbind(res$statsUp, gsStatsUp)
res$statsDn <- cbind(res$statsDn, gsStatsDn)
res$nGenes <- cbind(res$nGenes, nGenes)
res$nGenesUp <- cbind(res$nGenesUp, nGenesUp)
res$nGenesDn <- cbind(res$nGenesDn, nGenesDn)
res$pValuesAll <- cbind(res$pValuesAll, pValuesAll)
res$pValuesAllUp <- cbind(res$pValuesAllUp, pValuesAllUp)
res$pValuesAllDn <- cbind(res$pValuesAllDn, pValuesAllDn)
res$pValuesAbs <- cbind(res$pValuesAbs, pValuesAbs)
res$pValuesUp <- cbind(res$pValuesUp, pValuesUp)
res$pValuesDn <- cbind(res$pValuesDn, pValuesDn)
if(method == "fisher") res$statName = "X2"
else if(method == "stouffer") res$statName = "Z"
else if(method == "tailStrength") res$statName = "TS"
else if(method == "reporter") res$statName = "Z" # This is the raw Z-score.
else if(method == "wilcoxon") res$statName = "W"
else if(method == "wilcoxon_fast") res$statName = "W"
else if(method == "mean") res$statName = "mean"
else if(method == "median") res$statName = "median"
else if(method == "sum") res$statName = "sum"
else if(method == "maxmean") res$statName = "maxmean"
else if(method == "gsea") res$statName = "ES"
else if(method == "fgsea") res$statName = "ES"
else if(method == "page") res$statName = "Z"
return(res)
}
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Defines functions GSCstatBatch
GSCstatBatch <- function(statistics, statType, gsc, method, signMethod, gseaParam, signs, nPerm) {
# Create result list object:
res <- list()
res$statsAll <- vector()
res$statsAllTestUp <- vector()
res$statsAllTestDn <- vector()
res$statsAbs <- vector()
res$statsUp <- vector()
res$statsDn <- vector()
res$nGenes <- vector()
res$nGenesUp <- vector()
res$nGenesDn <- vector()
res$pValuesAll <- vector()
res$pValuesAllUp <- vector()
res$pValuesAllDn <- vector()
res$pValuesAbs <- vector()
res$pValuesUp <- vector()
res$pValuesDn <- vector()
iContrast <- 1 # Remnant from when multiple contrast were allowed
# Preallocate:
gsStatsAll <- rep(NA,length(gsc))
gsStatsAllTestUp <- rep(NA,length(gsc))
gsStatsAllTestDn <- rep(NA,length(gsc))
gsStatsAbs <- rep(NA,length(gsc))
gsStatsUp <- rep(NA,length(gsc))
gsStatsDn <- rep(NA,length(gsc))
nGenes <- rep(0,length(gsc))
nGenesUp <- rep(0,length(gsc))
nGenesDn <- rep(0,length(gsc))
pValuesAll <- rep(NA,length(gsc))
pValuesAllUp <- rep(NA,length(gsc))
pValuesAllDn <- rep(NA,length(gsc))
pValuesAbs <- rep(NA,length(gsc))
pValuesUp <- rep(NA,length(gsc))
pValuesDn <- rep(NA,length(gsc))
# Get statistics for current contrast:
statsContrast <- statistics[,iContrast]
if(statType %in% c("p-signed","F-signed")) {
signsContrast <- signs[,iContrast]
}
if(statType == "t") {
signsContrast <- sign(statsContrast)
}
# If possible, calculate "directional p-values":
if(method %in% c("stouffer","reporter","tailStrength","wilcoxon","wilcoxon_fast","mean","median","sum") & statType == "p-signed") {
statsContrastTestUp <- abs(statsContrast)
statsContrastTestUp[signsContrast > 0] <- statsContrastTestUp[signsContrast > 0]/2
statsContrastTestUp[signsContrast < 0] <- 1 - statsContrastTestUp[signsContrast < 0]/2
statsContrastTestUp[signsContrast == 0] <- NA
statsContrastTestDn <- 1 - statsContrastTestUp
# Fix zeros and ones in directional p-values:
statsContrastTestUp[statsContrastTestUp < 1e-100] <- 1e-100
statsContrastTestUp[statsContrastTestUp > 0.9999999999999999] <- 0.9999999999999999
statsContrastTestDn[statsContrastTestDn < 1e-100] <- 1e-100
statsContrastTestDn[statsContrastTestDn > 0.9999999999999999] <- 0.9999999999999999
}
# Loop through the gene-sets and calculate gene-set statistics (except from FGSEA which does its own looping, further down):
for(iGeneSet in 1:length(gsc)) {
#************************
# Fisher:
#************************
if(method == "fisher") {
# Get statistics for gene-set:
indGenesInSet <- names(statsContrast) %in% gsc[[iGeneSet]]
statsGenesInSet <- statsContrast[indGenesInSet]
nGenes[iGeneSet] <- length(statsGenesInSet)
if(nGenes[iGeneSet] > 0) {
# Genes up/dn (partly redundant code added later as a fix):
if(exists("signsContrast")) {
nGenesUp[iGeneSet] <- sum(signsContrast[indGenesInSet]>0)
nGenesDn[iGeneSet] <- sum(signsContrast[indGenesInSet]<0)
}
# "Mixed" gene-set statistic:
gsStatsAbs[iGeneSet] <- calcGeneSetStat(abs(statsGenesInSet), method)
# "Subset-up" gene-set statistic:
if(statType == "p-signed" & signMethod != "sampleperm") {
signsGenesInSet <- signsContrast[indGenesInSet]
sel <- statsGenesInSet[signsGenesInSet > 0]
nGenesUp[iGeneSet] <- length(sel)
if(nGenesUp[iGeneSet] > 0) {
gsStatsUp[iGeneSet] <- calcGeneSetStat(sel, method)
}
# "Subset-dn" gene-set statistic:
sel <- abs(statsGenesInSet[signsGenesInSet < 0])
nGenesDn[iGeneSet] <- length(sel)
if(nGenesDn[iGeneSet] > 0) {
gsStatsDn[iGeneSet] <- calcGeneSetStat(sel, method)
}
}
}
#************************
# Stouffer:
# Reporter:
# Tail strength:
#************************
} else if(method %in% c("stouffer","reporter","tailStrength")) {
# Get statistics for gene-set:
indGenesInSet <- names(statsContrast) %in% gsc[[iGeneSet]]
statsGenesInSet <- statsContrast[indGenesInSet]
nGenes[iGeneSet] <- length(statsGenesInSet)
if(nGenes[iGeneSet] > 0) {
# Genes up/dn (partly redundant code added later as a fix):
if(exists("signsContrast")) {
nGenesUp[iGeneSet] <- sum(signsContrast[indGenesInSet]>0)
nGenesDn[iGeneSet] <- sum(signsContrast[indGenesInSet]<0)
}
# "Directional" gene-set statistics:
if(statType == "p-signed") {
statsGenesInSetTestUp <- statsContrastTestUp[indGenesInSet]
statsGenesInSetTestDn <- statsContrastTestDn[indGenesInSet]
statsGenesInSetTestUp <- statsGenesInSetTestUp[!is.na(statsGenesInSetTestUp)]
statsGenesInSetTestDn <- statsGenesInSetTestDn[!is.na(statsGenesInSetTestDn)]
gsStatsAllTestUp[iGeneSet] <- calcGeneSetStat(statsGenesInSetTestUp, method)
gsStatsAllTestDn[iGeneSet] <- calcGeneSetStat(statsGenesInSetTestDn, method)
}
# "Mixed" gene-set statistic:
gsStatsAbs[iGeneSet] <- calcGeneSetStat(abs(statsGenesInSet), method)
# "Subset-up" gene-set statistic:
if(statType == "p-signed" & signMethod != "sampleperm") {
signsGenesInSet <- signsContrast[indGenesInSet]
sel <- statsGenesInSet[signsGenesInSet > 0]
nGenesUp[iGeneSet] <- length(sel)
if(nGenesUp[iGeneSet] > 0) {
gsStatsUp[iGeneSet] <- calcGeneSetStat(sel, method)
}
# "Subset-dn" gene-set statistic:
sel <- abs(statsGenesInSet[signsGenesInSet < 0])
nGenesDn[iGeneSet] <- length(sel)
if(nGenesDn[iGeneSet] > 0) {
gsStatsDn[iGeneSet] <- calcGeneSetStat(sel, method)
}
}
}
#************************
# Wilcoxon:
#************************
} else if(method == "wilcoxon") {
# Get statistics for gene-set:
indGenesInSet <- names(statsContrast) %in% gsc[[iGeneSet]]
statsGenesInSet <- statsContrast[indGenesInSet]
statsNotInSet <- statsContrast[!indGenesInSet]
if(statType %in% c("p-signed","F-signed")) {
signsGenesInSet <- signsContrast[indGenesInSet]
signsNotInSet <- signsContrast[!indGenesInSet]
}
nGenes[iGeneSet] <- length(statsGenesInSet)
if(nGenes[iGeneSet] > 0) {
# Genes up/dn (partly redundant code added later as a fix):
if(exists("signsContrast")) {
nGenesUp[iGeneSet] <- sum(signsContrast[indGenesInSet]>0)
nGenesDn[iGeneSet] <- sum(signsContrast[indGenesInSet]<0)
}
# "Directional" gene-set statistics:
if(statType == "p-signed") {
statsGenesInSetTestUp <- statsContrastTestUp[indGenesInSet]
statsGenesInSetTestDn <- statsContrastTestDn[indGenesInSet]
statsGenesInSetTestUp <- statsGenesInSetTestUp[!is.na(statsGenesInSetTestUp)]
statsGenesInSetTestDn <- statsGenesInSetTestDn[!is.na(statsGenesInSetTestDn)]
statsNotInSetTestUp <- statsContrastTestUp[!indGenesInSet]
statsNotInSetTestDn <- statsContrastTestDn[!indGenesInSet]
statsNotInSetTestUp <- statsNotInSetTestUp[!is.na(statsNotInSetTestUp)]
statsNotInSetTestDn <- statsNotInSetTestDn[!is.na(statsNotInSetTestDn)]
tmp <- calcGeneSetStat(statsGenesInSetTestUp, "wilcoxon_less", statsNotInSetTestUp)
gsStatsAllTestUp[iGeneSet] <- tmp[1]
pValuesAllUp[iGeneSet] <- tmp[2]
tmp <- calcGeneSetStat(statsGenesInSetTestDn, "wilcoxon_less", statsNotInSetTestDn)
gsStatsAllTestDn[iGeneSet] <- tmp[1]
pValuesAllDn[iGeneSet] <- tmp[2]
} else if(statType == "t") {
tmp <- calcGeneSetStat(statsGenesInSet, "wilcoxon_two.sided", statsNotInSet)
gsStatsAll[iGeneSet] <- tmp[1]
#pValuesAll[iGeneSet] <- tmp[2]
tmp <- calcGeneSetStat(statsGenesInSet, "wilcoxon_greater", statsNotInSet)
pValuesAllUp[iGeneSet] <- tmp[2]
tmp <- calcGeneSetStat(statsGenesInSet, "wilcoxon_less", statsNotInSet)
pValuesAllDn[iGeneSet] <- tmp[2]
}
# "Mixed" gene-set statistic:
if(statType %in% c("p","p-signed")) {
tmp <- calcGeneSetStat(abs(statsGenesInSet), "wilcoxon_less", abs(statsNotInSet))
gsStatsAbs[iGeneSet] <- tmp[1]
pValuesAbs[iGeneSet] <- tmp[2]
} else if(statType %in% c("t","F","F-signed")) {
tmp <- calcGeneSetStat(abs(statsGenesInSet), "wilcoxon_greater", abs(statsNotInSet))
gsStatsAbs[iGeneSet] <- tmp[1]
pValuesAbs[iGeneSet] <- tmp[2]
}
# "Subset-up" gene-set statistic:
if(statType %in% c("t","p-signed","F-signed") & signMethod != "sampleperm") {
if(statType == "t") {
sel <- statsGenesInSet[statsGenesInSet > 0]
} else {
sel <- statsGenesInSet[signsGenesInSet > 0]
}
nGenesUp[iGeneSet] <- length(sel)
if(nGenesUp[iGeneSet] > 0) {
if(statType == "p-signed") {
tmp <- calcGeneSetStat(sel, "wilcoxon_less", statsNotInSet[signsNotInSet > 0])
gsStatsUp[iGeneSet] <- tmp[1]
pValuesUp[iGeneSet] <- tmp[2]
} else if(statType == "t") {
tmp <- calcGeneSetStat(sel, "wilcoxon_greater", statsNotInSet[statsNotInSet > 0])
gsStatsUp[iGeneSet] <- tmp[1]
pValuesUp[iGeneSet] <- tmp[2]
} else if(statType == "F-signed") {
tmp <- calcGeneSetStat(sel, "wilcoxon_greater", statsNotInSet[signsNotInSet > 0])
gsStatsUp[iGeneSet] <- tmp[1]
pValuesUp[iGeneSet] <- tmp[2]
}
}
# "Subset-dn" gene-set statistic:
if(statType == "t") {
sel <- abs(statsGenesInSet[statsGenesInSet < 0])
} else {
sel <- abs(statsGenesInSet[signsGenesInSet < 0])
}
nGenesDn[iGeneSet] <- length(sel)
if(nGenesDn[iGeneSet] > 0) {
if(statType == "p-signed") {
tmp <- calcGeneSetStat(sel, "wilcoxon_less", abs(statsNotInSet[signsNotInSet < 0]))
gsStatsDn[iGeneSet] <- tmp[1]
pValuesDn[iGeneSet] <- tmp[2]
} else if(statType == "t") {
tmp <- calcGeneSetStat(sel, "wilcoxon_greater", abs(statsNotInSet[statsNotInSet < 0]))
gsStatsDn[iGeneSet] <- tmp[1]
pValuesDn[iGeneSet] <- tmp[2]
} else if(statType == "F-signed") {
tmp <- calcGeneSetStat(sel, "wilcoxon_greater", abs(statsNotInSet[signsNotInSet < 0]))
gsStatsDn[iGeneSet] <- tmp[1]
pValuesDn[iGeneSet] <- tmp[2]
}
}
}
}
#************************
# Wilcoxon, fast (only used by GSCstatSamplePerm):
#************************
} else if(method == "wilcoxon_fast") {
# Get statistics for gene-set:
indGenesInSet <- names(statsContrast) %in% gsc[[iGeneSet]]
statsGenesInSet <- statsContrast[indGenesInSet]
statsNotInSet <- statsContrast[!indGenesInSet]
if(statType %in% c("p-signed","F-signed")) {
signsGenesInSet <- signsContrast[indGenesInSet]
signsNotInSet <- signsContrast[!indGenesInSet]
}
nGenes[iGeneSet] <- length(statsGenesInSet)
if(nGenes[iGeneSet] > 0) {
# Genes up/dn (partly redundant code added later as a fix):
if(exists("signsContrast")) {
nGenesUp[iGeneSet] <- sum(signsContrast[indGenesInSet]>0)
nGenesDn[iGeneSet] <- sum(signsContrast[indGenesInSet]<0)
}
# "Directional" gene-set statistics:
if(statType == "p-signed") {
statsGenesInSetTestUp <- statsContrastTestUp[indGenesInSet]
statsGenesInSetTestDn <- statsContrastTestDn[indGenesInSet]
statsGenesInSetTestUp <- statsGenesInSetTestUp[!is.na(statsGenesInSetTestUp)]
statsGenesInSetTestDn <- statsGenesInSetTestDn[!is.na(statsGenesInSetTestDn)]
statsNotInSetTestUp <- statsContrastTestUp[!indGenesInSet]
statsNotInSetTestDn <- statsContrastTestDn[!indGenesInSet]
statsNotInSetTestUp <- statsNotInSetTestUp[!is.na(statsNotInSetTestUp)]
statsNotInSetTestDn <- statsNotInSetTestDn[!is.na(statsNotInSetTestDn)]
gsStatsAllTestUp[iGeneSet] <- calcGeneSetStat(statsGenesInSetTestUp, "wilcoxon_fast", statsNotInSetTestUp)
gsStatsAllTestDn[iGeneSet] <- calcGeneSetStat(statsGenesInSetTestDn, "wilcoxon_fast", statsNotInSetTestDn)
} else if(statType == "t") {
gsStatsAll[iGeneSet] <- calcGeneSetStat(statsGenesInSet, "wilcoxon_fast", statsNotInSet)
}
# "Mixed" gene-set statistic:
if(statType %in% c("p","p-signed")) {
gsStatsAbs[iGeneSet] <- calcGeneSetStat(abs(statsGenesInSet), "wilcoxon_fast", abs(statsNotInSet))
} else if(statType %in% c("t","F","F-signed")) {
gsStatsAbs[iGeneSet] <- calcGeneSetStat(abs(statsGenesInSet), "wilcoxon_fast", abs(statsNotInSet))
}
# "Subset-up" gene-set statistic:
if(statType %in% c("t","p-signed","F-signed") & signMethod != "sampleperm") {
if(statType == "t") {
sel <- statsGenesInSet[statsGenesInSet > 0]
} else {
sel <- statsGenesInSet[signsGenesInSet > 0]
}
nGenesUp[iGeneSet] <- length(sel)
if(nGenesUp[iGeneSet] > 0) {
if(statType == "p-signed") {
gsStatsUp[iGeneSet] <- calcGeneSetStat(sel, "wilcoxon_fast", statsNotInSet[signsNotInSet > 0])
} else if(statType == "t") {
gsStatsUp[iGeneSet] <- calcGeneSetStat(sel, "wilcoxon_fast", statsNotInSet[statsNotInSet > 0])
} else if(statType == "F-signed") {
gsStatsUp[iGeneSet] <- calcGeneSetStat(sel, "wilcoxon_fast", statsNotInSet[signsNotInSet > 0])
}
}
# "Subset-dn" gene-set statistic:
if(statType == "t") {
sel <- abs(statsGenesInSet[statsGenesInSet < 0])
} else {
sel <- abs(statsGenesInSet[signsGenesInSet < 0])
}
nGenesDn[iGeneSet] <- length(sel)
if(nGenesDn[iGeneSet] > 0) {
if(statType == "p-signed") {
gsStatsDn[iGeneSet] <- calcGeneSetStat(sel, "wilcoxon_fast", abs(statsNotInSet[signsNotInSet < 0]))
} else if(statType == "t") {
gsStatsDn[iGeneSet] <- calcGeneSetStat(sel, "wilcoxon_fast", abs(statsNotInSet[statsNotInSet < 0]))
} else if(statType == "F-signed") {
gsStatsDn[iGeneSet] <- calcGeneSetStat(sel, "wilcoxon_fast", abs(statsNotInSet[signsNotInSet < 0]))
}
}
}
}
#************************
# Mean:
# Median:
# Sum:
#************************
} else if(method %in% c("mean","median","sum")) {
# Get statistics for gene-set:
indGenesInSet <- names(statsContrast) %in% gsc[[iGeneSet]]
statsGenesInSet <- statsContrast[indGenesInSet]
if(statType %in% c("p-signed","F-signed")) {
signsGenesInSet <- signsContrast[indGenesInSet]
}
nGenes[iGeneSet] <- length(statsGenesInSet)
if(nGenes[iGeneSet] > 0) {
# Genes up/dn (partly redundant code added later as a fix):
if(exists("signsContrast")) {
nGenesUp[iGeneSet] <- sum(signsContrast[indGenesInSet]>0)
nGenesDn[iGeneSet] <- sum(signsContrast[indGenesInSet]<0)
}
# "Directional" gene-set statistics:
if(statType == "p-signed") {
statsGenesInSetTestUp <- statsContrastTestUp[indGenesInSet]
statsGenesInSetTestDn <- statsContrastTestDn[indGenesInSet]
statsGenesInSetTestUp <- statsGenesInSetTestUp[!is.na(statsGenesInSetTestUp)]
statsGenesInSetTestDn <- statsGenesInSetTestDn[!is.na(statsGenesInSetTestDn)]
gsStatsAllTestUp[iGeneSet] <- calcGeneSetStat(statsGenesInSetTestUp, method)
gsStatsAllTestDn[iGeneSet] <- calcGeneSetStat(statsGenesInSetTestDn, method)
} else if(statType == "t") {
gsStatsAll[iGeneSet] <- calcGeneSetStat(statsGenesInSet, method)
}
# "Mixed" gene-set statistic:
gsStatsAbs[iGeneSet] <- calcGeneSetStat(abs(statsGenesInSet), method)
# "Subset-up" gene-set statistic:
if(statType %in% c("p-signed","t","F-signed") & signMethod != "sampleperm") {
if(statType == "t") {
sel <- statsGenesInSet[statsGenesInSet > 0]
} else {
sel <- statsGenesInSet[signsGenesInSet > 0]
}
nGenesUp[iGeneSet] <- length(sel)
if(nGenesUp[iGeneSet] > 0) {
gsStatsUp[iGeneSet] <- calcGeneSetStat(sel, method)
}
# "Subset-dn" gene-set statistic:
if(statType == "t") {
sel <- abs(statsGenesInSet[statsGenesInSet < 0])
} else {
sel <- abs(statsGenesInSet[signsGenesInSet < 0])
}
nGenesDn[iGeneSet] <- length(sel)
if(nGenesDn[iGeneSet] > 0) {
gsStatsDn[iGeneSet] <- calcGeneSetStat(sel, method)
}
}
}
#************************
# Maxmean:
#************************
} else if(method == "maxmean") {
# Get statistics for gene-set:
indGenesInSet <- names(statsContrast) %in% gsc[[iGeneSet]]
statsGenesInSet <- statsContrast[indGenesInSet]
nGenes[iGeneSet] <- length(statsGenesInSet)
if(nGenes[iGeneSet] > 0) {
# Genes up/dn (partly redundant code added later as a fix):
if(exists("signsContrast")) {
nGenesUp[iGeneSet] <- sum(signsContrast[indGenesInSet]>0)
nGenesDn[iGeneSet] <- sum(signsContrast[indGenesInSet]<0)
}
# "Mixed" gene-set statistic:
gsStatsAbs[iGeneSet] <- calcGeneSetStat(statsGenesInSet, method)
}
#************************
# GSEA:
#************************
} else if(method == "gsea") {
# Get statistics for gene-set:
statsContrastSorted <- sort(statsContrast,decreasing=TRUE)
indGenesInSet <- which(names(statsContrastSorted) %in% gsc[[iGeneSet]])
nGenes[iGeneSet] <- length(indGenesInSet)
if(nGenes[iGeneSet] > 0) {
# Genes up/dn (partly redundant code added later as a fix):
if(exists("signsContrast")) {
#nGenesUp[iGeneSet] <- sum(signsContrast[indGenesInSet]>0)
#nGenesDn[iGeneSet] <- sum(signsContrast[indGenesInSet]<0)
nGenesUp[iGeneSet] <- sum(statsContrastSorted[indGenesInSet]>0)
nGenesDn[iGeneSet] <- sum(statsContrastSorted[indGenesInSet]<0)
}
# "Directional" gene-set statistic:
gsStatsAll[iGeneSet] <- calcGeneSetStat(indGenesInSet, method, statsContrastSorted, gseaParam)
}
#************************
# Page:
#************************
} else if(method == "page") {
# Get statistic for gene-set:
indGenesInSet <- names(statsContrast) %in% gsc[[iGeneSet]]
statsGenesInSet <- statsContrast[indGenesInSet]
nGenes[iGeneSet] <- length(statsGenesInSet)
if(nGenes[iGeneSet] > 0) {
# Genes up/dn (partly redundant code added later as a fix):
if(exists("signsContrast")) {
nGenesUp[iGeneSet] <- sum(signsContrast[indGenesInSet]>0)
nGenesDn[iGeneSet] <- sum(signsContrast[indGenesInSet]<0)
}
# "Directional" gene-set statistics:
gsStatsAll[iGeneSet] <- calcGeneSetStat(statsGenesInSet, method, statsContrast)
}
}
}
#************************
# FGSEA:
#************************
if(method == "fgsea") {
# Run FGSEA using the fgsea package:
tmp <- fgsea(gsc, statsContrast, nperm=nPerm, minSize=1, maxSize=Inf, nproc=0, gseaParam=gseaParam)
# Sort the result table so it matches the original gene-set order:
tmp <- tmp[match(tmp$pathway, names(gsc)),]
# Extract the results:
gsStatsAll <- tmp$ES
pValuesAllUp <- rep(NA, length(tmp$pval))
pValuesAllDn <- pValuesAllUp
pValuesAllUp[gsStatsAll>=0] <- tmp$pval[gsStatsAll>=0]
pValuesAllDn[gsStatsAll<0] <- tmp$pval[gsStatsAll<0]
# Calculate number of genes:
nGenes <- unlist(lapply(gsc, length))
nGenesUp <- unlist(lapply(gsc, function(x) sum(signsContrast[x]>0)))
nGenesDn <- unlist(lapply(gsc, function(x) sum(signsContrast[x]<0)))
}
#--------------------
# Save results:
res$statsAll <- cbind(res$statsAll, gsStatsAll)
res$statsAllTestUp <- cbind(res$statsAllTestUp, gsStatsAllTestUp)
res$statsAllTestDn <- cbind(res$statsAllTestDn, gsStatsAllTestDn)
res$statsAbs <- cbind(res$statsAbs, gsStatsAbs)
res$statsUp <- cbind(res$statsUp, gsStatsUp)
res$statsDn <- cbind(res$statsDn, gsStatsDn)
res$nGenes <- cbind(res$nGenes, nGenes)
res$nGenesUp <- cbind(res$nGenesUp, nGenesUp)
res$nGenesDn <- cbind(res$nGenesDn, nGenesDn)
res$pValuesAll <- cbind(res$pValuesAll, pValuesAll)
res$pValuesAllUp <- cbind(res$pValuesAllUp, pValuesAllUp)
res$pValuesAllDn <- cbind(res$pValuesAllDn, pValuesAllDn)
res$pValuesAbs <- cbind(res$pValuesAbs, pValuesAbs)
res$pValuesUp <- cbind(res$pValuesUp, pValuesUp)
res$pValuesDn <- cbind(res$pValuesDn, pValuesDn)
if(method == "fisher") res$statName = "X2"
else if(method == "stouffer") res$statName = "Z"
else if(method == "tailStrength") res$statName = "TS"
else if(method == "reporter") res$statName = "Z" # This is the raw Z-score.
else if(method == "wilcoxon") res$statName = "W"
else if(method == "wilcoxon_fast") res$statName = "W"
else if(method == "mean") res$statName = "mean"
else if(method == "median") res$statName = "median"
else if(method == "sum") res$statName = "sum"
else if(method == "maxmean") res$statName = "maxmean"
else if(method == "gsea") res$statName = "ES"
else if(method == "fgsea") res$statName = "ES"
else if(method == "page") res$statName = "Z"
return(res)
}
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