[BioC] GSEAbase example? [was KEGG & hyperGTest: an example?]

[Paul Shannon]

Hi Robert,

Last week you wrote:

    The GSEAbase package is I think a much better way to do that, and is
    actually intended for such purposes.

where the 'that' you refer to is is my use (abuse...) of the Category
package to find shared GO categories, KEGG pathways, and PFAM domains  
among
(typically) 30-100 proteins identified by shotgun proteomics.

I'm sorry to be so slow on the uptake here, but after reading the  
GSEAbase vignette,
I am no closer to understanding how to do the GSEAbase equivalent of  
the following
quick method for finding that two of my proteins share the PF00069  
domain:

   proteins = c ("YLR113W", "YBR069C", "YBR279W", "YCR030C",  
"YDR168W", "YNR031C")

   params = new ("PFAMHyperGParams", geneIds = proteins,
                 universeGeneIds = character(0), annotation = "YEAST",
                 pvalueCutoff = 1.0, testDirection = "over")

   hgr.yeast.pfam = hyperGTest (params)

   subset (summary (hgr.yeast.pfam), Count >= 2)

            PFAMID      Pvalue OddsRatio  ExpCount Count Size    Term
   PF00069 PF00069 0.006570706  24.98214 0.1321280     2  114 PF00069


Is there an example you could refer me to?

Thanks!

  - Paul





>> 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.
>  The GSEAbase package is I think a much better way to do that, and  
> is actually intended for such purposes.