[BioC] KEGG & hyperGTest: an example?

[Seth Falcon]

Paul Shannon <pshannon at systemsbiology.org> writes:

> Can anyone direct me to an example of using hyperGTest with a  
> KEGGHyperGParams?
>
> My organism is yeast and -- since my experimental data is from  
> proteomics -- I
> have been happy using the YEAST annotation package, rather than  
> annotation
> for a particular chip:
>
>    params = new ("GOHyperGParams", geneIds = unique (genes),
>                  universeGeneIds = character (0), annotation = "YEAST",
>                  ontology = ontology, pvalueCutoff = pvalue,  
> conditional = FALSE,
>                  testDirection = "over")
>
>    hgr = hyperGTest (params)
>
> I'd be delighted to find a similar example for yeast & KEGG.  My own  
> experiments
> and web searching didn't get me far.

Does this not work?

>    params = new("KEGGHyperGParams", geneIds = unique(genes),
>                 universeGeneIds = character(0), annotation = "YEAST",
>                 ontology = ontology, pvalueCutoff = pvalue,  
>                 conditional = FALSE,
>                 testDirection = "over")

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

+ seth

-- 
Seth Falcon | seth at userprimary.net | blog: http://userprimary.net/user/