## ----message=FALSE------------------------------------------------------------ library(fgsea) library(data.table) library(ggplot2) ## ----echo=FALSE--------------------------------------------------------------- library(BiocParallel) register(SerialParam()) ## ----------------------------------------------------------------------------- data(examplePathways) data(exampleRanks) set.seed(42) ## ----------------------------------------------------------------------------- fgseaRes <- fgsea(pathways = examplePathways, stats = exampleRanks, minSize = 15, maxSize = 500) ## ----------------------------------------------------------------------------- head(fgseaRes[order(pval), ]) ## ----------------------------------------------------------------------------- fgseaRes <- fgsea(pathways = examplePathways, stats = exampleRanks, eps = 0.0, minSize = 15, maxSize = 500) head(fgseaRes[order(pval), ]) ## ---- 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, warning=FALSE------------------ collapsedPathways <- collapsePathways(fgseaRes[order(pval)][padj < 0.01], examplePathways, exampleRanks) mainPathways <- fgseaRes[pathway %in% collapsedPathways$mainPathways][ order(-NES), pathway] plotGseaTable(examplePathways[mainPathways], exampleRanks, fgseaRes, gseaParam = 0.5) ## ----message=FALSE------------------------------------------------------------ fwrite(fgseaRes, file="fgseaRes.txt", sep="\t", sep2=c("", " ", "")) ## ----message=FALSE------------------------------------------------------------ library(org.Mm.eg.db) fgseaResMain <- fgseaRes[match(mainPathways, pathway)] fgseaResMain[, leadingEdge := mapIdsList( x=org.Mm.eg.db, keys=leadingEdge, keytype="ENTREZID", column="SYMBOL")] fwrite(fgseaResMain, file="fgseaResMain.txt", sep="\t", sep2=c("", " ", "")) ## ----message=FALSE, warning=FALSE--------------------------------------------- pathways <- reactomePathways(names(exampleRanks)) fgseaRes <- fgsea(pathways, exampleRanks, maxSize=500) head(fgseaRes) ## ----------------------------------------------------------------------------- rnk.file <- system.file("extdata", "naive.vs.th1.rnk", package="fgsea") gmt.file <- system.file("extdata", "mouse.reactome.gmt", package="fgsea") ## ----------------------------------------------------------------------------- ranks <- read.table(rnk.file, header=TRUE, colClasses = c("character", "numeric")) ranks <- setNames(ranks$t, ranks$ID) str(ranks) ## ----------------------------------------------------------------------------- pathways <- gmtPathways(gmt.file) str(head(pathways)) ## ----warning=FALSE------------------------------------------------------------ fgseaRes <- fgsea(pathways, ranks, minSize=15, maxSize=500) head(fgseaRes)