[BioC] GOStats: HyperGTest question

[Johannes Graumann]

Hello,

When doing this:

> params <- new(
>       "GOHyperGParams",
>       geneIds=ipilist,
>       universeGeneIds=names(as.list(get(paste(annotation,"GO",sep="")))),
>       annotation=annotation,
>       ontology="BP",
>       pvalueCutoff=0.001,
>       conditional=FALSE,
>       testDirection = "over"
>     )
>     hgOver <- hyperGTest(params)

with 'ipilist' being a vector of IPI ids, and 'annotation' being a
AnnBuilder package I build to map go terms to IPI ids via EntrezIDs,
I get the following error:

> Error in getUniverseHelper(probes, lib, entrezIds) :
>         No Entrez Gene ids left in universe

The 'universe' construct is supposed to return all IPI ids from the
annotation package.

Please enlighten me as to where I err!

Something else: "GOHyperGParams" is not well documented on my system:

> ?GOHyperGParams-class

gets me this:

> Error in eval(expr, envir, enclos) : object "GOHyperGParams" not found
> Error in .helpForCall(e1Expr, parent.frame()) :
>         error in trying to evaluate the expression for argument 'e1' 
> (GOHyperGParams) 

My specific questions are:
- is there an option like "ontology='all'"?
- is there an option like "testDirection='both'"?

Thanks for any hints, Joh