The GOHyperGParams takes an ontology argument:

ontology: A string specifying the GO ontology to use. Must be one of "BP", "CC", or "MF".

From the thread GO analysis, BP, CC, MF separate or combined I learned that one should ideally combine the ontologies if you are interested in all three. But I see no way of doing that.

Should you really combine all three ontologies, and if so, how do you do it?

Ps. if you attempt something like

params <- new("GOHyperGParams", geneIds = beste, universeGeneIds = unie, ontology = "BP, CC, MF", pvalueCutoff = 0.5, conditional = FALSE, testDirection = "over")

you get the following error message:

Error in match.arg(ontology, c("BP", "CC", "MF")) : 'arg' should be one of “BP”, “CC”, “MF”