[BioC] KEGG & hyperGTest: an example?

[Paul Shannon]

With Seth's prompting :} I went back and fiddled a while longer with
my KEGGHyperGParams.  I eventually found the right combination, which
I include below (along with a PFAMHyperGParams example) in case it
might be useful to someone.

As for Seth's other comment:

> (although I'm confused why specifying zero-length for universeGeneIds
> makes any sense...)

I think it does make sense as long as the goal of the analysis is  
annotation,
rather than enrichment.  The Category package is a very handy way
to discover, for example, which GO terms, KEGG pathways, and
PFAM domains are shared among proteins, as I try to elucidate the
results of experiments in phosphoproteomics.


---- KEGG and YEAST example

   genes = c("YLR113W", "YFL026W")
   params = new("KEGGHyperGParams", geneIds = unique(genes),
                universeGeneIds = character(0), annotation = "YEAST",
                pvalueCutoff = 0.1, testDirection = "over")

   hgr.yeast.kegg = hyperGTest(params)

--- PFAM and YEAST example

    genes = c("YLR113W", "YNR031C")
    params = new("PFAMHyperGParams", geneIds = unique(genes),
                 universeGeneIds = character(0), annotation = "YEAST",
                 pvalueCutoff = 0.1, testDirection = "over")

    hgr.yeast.pfam = hyperGTest (params)


> Does this not work?
>
>>    params = new("KEGGHyperGParams", geneIds = unique(genes),
>>                 universeGeneIds = character(0), annotation = "YEAST",
>>                 ontology = ontology, pvalueCutoff = pvalue,
>>                 conditional = FALSE,
>>                 testDirection = "over")
>