An example of calculate GO enrichment by topGO

Not required Entrez Gene IDs, this example takes Ensembl Gene IDs and calcuates GO enrichment.

# Install packages, if not
# source('http://www.bioconductor.org/biocLite.R') biocLite(c('biomaRt',
# 'topGO', 'org.Mm.eg.db'))
library(biomaRt)
library(org.Mm.eg.db)
library(topGO)

all_genes <- rep(c(0, 1, 1), each = 10)

names(all_genes) <- c("ENSMUSG00000031167", "ENSMUSG00000022443", "ENSMUSG00000055762", 
    "ENSMUSG00000031328", "ENSMUSG00000026728", "ENSMUSG00000029722", "ENSMUSG00000059208", 
    "ENSMUSG00000017404", "ENSMUSG00000003970", "ENSMUSG00000019210", "ENSMUSG00000024966", 
    "ENSMUSG00000024197", "ENSMUSG00000030847", "ENSMUSG00000004264", "ENSMUSG00000041959", 
    "ENSMUSG00000032643", "ENSMUSG00000042520", "ENSMUSG00000028484", "ENSMUSG00000022186", 
    "ENSMUSG00000027593", "ENSMUSG00000019795", "ENSMUSG00000021134", "ENSMUSG00000026956", 
    "ENSMUSG00000022982", "ENSMUSG00000027162", "ENSMUSG00000024668", "ENSMUSG00000000168", 
    "ENSMUSG00000022234", "ENSMUSG00000024991", "ENSMUSG00000018697")

GOdata <- new("topGOdata", ontology = "BP", allGenes = all_genes, geneSel = function(p) p < 
    0.01, description = "Test", annot = annFUN.org, mapping = "org.Mm.eg.db", 
    ID = "Ensembl")

resultFisher <- runTest(GOdata, algorithm = "classic", statistic = "fisher")
GenTable(GOdata, classicFisher = resultFisher, topNodes = 10)