I have run a GO enrichment analysis using enrichGO() for all 3 onthologies at once:
analysis <- enrichGO(gene = names_down_uniprot, OrgDb = "org.Mm.eg.db", keyType = "UNIPROT", ont = "ALL", pvalueCutoff = 0.05, pAdjustMethod = "fdr", universe = background_uniprot, qvalueCutoff = 0.25, minGSSize = 10, maxGSSize = 500, readable = FALSE, pool = FALSE)
The result looks good and as expected.
Do anyone now how to subset this results for a specific onthology? My idea is to represent graphically (using barplot, cnetplot, etc) only one of of them (in particular BP).
Thanks in advance,