Listifying KEGG and GO gene sets

kegg_and_go_gene_sets.R

library(limma)
library(AnnotationDbi)
library(GO.db)
library(org.Hs.eg.db)

# KEGG
kegg.names <- getKEGGPathwayNames("hsa", remove.qualifier = TRUE)
kegg.sets <- getGeneKEGGLinks("hsa", convert = TRUE)
kegg.gsc <- with(kegg.sets, split(GeneID, PathwayID))
names(kegg.gsc) <- kegg.names[
  match(names(kegg.gsc), kegg.names$PathwayID), "Description"]

# GO
go.sets <- AnnotationDbi::toTable(
  org.Hs.egGO2ALLEGS)[, c("gene_id", "go_id", "Ontology")]
go.names <- AnnotationDbi::mapIds(GO.db::GO.db, 
        keys = unique(go.sets$go_id), keytype = "GOID", column = "TERM")
go.gsc <- with(go.sets, split(gene_id, go_id))
names(go.gsc) <- go.names[names(go.gsc)]