Nothing
##This function performs a Mann-Whitney test for shift in location of
##genes from gene sets, on a pair of phenotypes. It looks for gene sets
##that are represented towards the 2 different ends of two ranked lists
##of genes, i.e. whose phenotype distribution is located around two
##different values in the two phenotypes list, rather than spread on
##the whole list in both lists.
pairwisePhenoMannWhit <- function(gl1, gl2, gsc, minGeneSetSize = 15,
pAdjustMethod = "BH") {
##check arguments
paraCheck("genelist", gl1)
paraCheck("genelist", gl2)
paraCheck("gsc", gsc)
paraCheck("minGeneSetSize", minGeneSetSize)
paraCheck("pAdjustMethod", pAdjustMethod)
wilcox.pval <- unlist(lapply(gsc, function(gs) {
gl1.gs <- match(gs, names(gl1))
gl1.gs <- gl1.gs[!is.na(gl1.gs)]
gl2.gs <- match(gs, names(gl2))
gl2.gs <- gl2.gs[!is.na(gl2.gs)]
if(length(gl1.gs >= minGeneSetSize) &&
length(gl2.gs >= minGeneSetSize)) {
wilcox.test(x = gl1[gl1.gs],
y = gl2[gl2.gs], alternative = "two.sided")$p.value
}
}))
wilcox.pval <- wilcox.pval[order(wilcox.pval)]
a.p <- p.adjust(wilcox.pval, method = pAdjustMethod)
wilcox.pval.table <- cbind(wilcox.pval, a.p)
rownames(wilcox.pval.table) <- names(wilcox.pval)
colnames(wilcox.pval.table) <- c("P.value", "Adjusted.p.value")
return(wilcox.pval.table)
}
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