[BioC] KEGG & hyperGTest: an example?

[Robert Gentleman]

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

  best wishes
    Robert


> 
> ---- 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")
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org