gsea.R

if (!requireNamespace("BiocManager", quietly=TRUE))
  install.packages("BiocManager")
BiocManager::install("fgsea")
library(fgsea)
data(examplePathways)
data(exampleRanks)
fgseaRes <- fgsea(pathways = examplePathways, 
                  stats = exampleRanks,
                  minSize=15,
                  maxSize=500,
                  nperm=10000)
head(fgseaRes[order(pval), ])
sum(fgseaRes[, padj < 0.01])

plotEnrichment(examplePathways[["5991130_Programmed_Cell_Death"]],
               exampleRanks) + labs(title="Programmed Cell Death")

topPathwaysUp <- fgseaRes[ES > 0][head(order(pval), n=10), pathway]
topPathwaysDown <- fgseaRes[ES < 0][head(order(pval), n=10), pathway]
topPathways <- c(topPathwaysUp, rev(topPathwaysDown))
plotGseaTable(examplePathways[topPathways], exampleRanks, fgseaRes, 
              gseaParam = 0.5)

collapsedPathways <- collapsePathways(fgseaRes[order(pval)][padj < 0.01], 
                                      examplePathways, exampleRanks)
mainPathways <- fgseaRes[pathway %in% collapsedPathways$mainPathways][
  order(-NES), pathway]
plotGseaTable(examplePathways[mainPathways], exampleRanks, fgseaRes, 
              gseaParam = 0.5)

library(org.Mm.eg.db)
fgseaResMain <- fgseaRes[match(mainPathways, pathway)]
fgseaResMain[, leadingEdge := lapply(leadingEdge, mapIds, x=org.Mm.eg.db, keytype="ENTREZID", column="SYMBOL")]
fwrite(fgseaResMain, file="fgseaResMain.txt", sep="\t", sep2=c("", " ", ""))

pathways <- reactomePathways(names(exampleRanks))
fgseaRes <- fgsea(pathways, exampleRanks, nperm=1000, maxSize=500)
head(fgseaRes)