inst/gse19429_gsea.R

In fgsea: Fast Gene Set Enrichment Analysis

library(fgsea)
library(limma)
library(GEOquery)
es <- getGEO("GSE19429", getGPL = FALSE)[[1]]
exprs(es) <- normalizeBetweenArrays(log2(exprs(es)+1), method="quantile")
es <- es[!grepl("///", fData(es)$`Gene ID`), ]
es <- es[fData(es)$`Gene ID` != "", ]
es <- es[order(apply(exprs(es), 1, mean), decreasing=TRUE), ]
es <- es[!duplicated(fData(es)$`Gene ID`), ]
rownames(es) <- fData(es)$`Gene ID`

pathways <- reactomePathways(rownames(es))
mat <- exprs(es)
labels <- as.numeric(as.factor(gsub(" .*", "", es$title)))

fgseaRes <- fgseaLabel(pathways, mat, labels, nperm = 1000, minSize = 15, maxSize = 500)