## ----echo=F, message=F--------------------------------------------------- library(fgsea) library(data.table) library(ggplot2) ## ------------------------------------------------------------------------ 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]) ## ---- fig.width=7, fig.height=4------------------------------------------ plotEnrichment(examplePathways[["5991130_Programmed_Cell_Death"]], exampleRanks) + labs(title="Programmed Cell Death") ## ---- fig.width=7, fig.height=8, fig.retina=2---------------------------- 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) ## ---- fig.width=7, fig.height=8, fig.retina=2---------------------------- collapsedPathways <- collapsePathways(fgseaRes[order(pval)][padj < 0.01], examplePathways, exampleRanks) mainPathways <- fgseaRes[pathway %in% collapsedPathways$mainPathways][ order(-NES), pathway] plotGseaTable(examplePathways[mainPathways], exampleRanks, fgseaRes, gseaParam = 0.5) ## ----message=FALSE------------------------------------------------------- library(data.table) fwrite(fgseaRes, file="fgseaRes.txt", sep="\t", sep2=c("", " ", "")) ## ----message=FALSE------------------------------------------------------- library(org.Mm.eg.db) fgseaResMain <- fgseaRes[match(mainPathways, pathway)] fgseaResMain[, leadingEdge := lapply(leadingEdge, mapIds, x=org.Mm.eg.db, keytype="ENTREZID", column="SYMBOL")] fwrite(fgseaResMain, file="fgseaResMain.txt", sep="\t", sep2=c("", " ", "")) ## ----message=F----------------------------------------------------------- pathways <- reactomePathways(names(exampleRanks)) fgseaRes <- fgsea(pathways, exampleRanks, nperm=1000, maxSize=500) head(fgseaRes) ## ------------------------------------------------------------------------ rnk.file <- system.file("extdata", "naive.vs.th1.rnk", package="fgsea") gmt.file <- system.file("extdata", "mouse.reactome.gmt", package="fgsea") ## ------------------------------------------------------------------------ ranks <- read.table(rnk.file, header=TRUE, colClasses = c("character", "numeric")) ranks <- setNames(ranks$t, ranks$ID) str(ranks) ## ------------------------------------------------------------------------ pathways <- gmtPathways(gmt.file) str(head(pathways)) ## ------------------------------------------------------------------------ fgseaRes <- fgsea(pathways, ranks, minSize=15, maxSize=500, nperm=1000) head(fgseaRes)