hyperGTest with org.Sc.sgd.db problem

Question

[andrejk]

I try to annotate ENTREZID identifiers with GO categories and apply hyperGTest() function. Using the following example from https://support.bioconductor.org/p/64862/ everything works fine:

library(org.Sc.sgd.db)
univ <- unique(keys(org.Sc.sgd.db))
genes <- univ[sample(1:length(univ), 250)]
p <- new("GOHyperGParams", geneIds = genes, universeGeneIds = univ, ontology = "BP", annotation = "org.Sc.sgd.db")
hyp <- hyperGTest(p)
head(summary(hyp))

I have no idea what are keys in the presented example. How can I instead use ENTREZID identifiers as keys in my testing?

Answer 1

[EagleEye]

Try this tool,

Gene Set Clustering based on Functional annotation (GeneSCF)