[BioC] KEGG & hyperGTest: an example?

Paul Shannon pshannon at systemsbiology.org
Tue Oct 23 19:09:09 CEST 2007


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.

Thanks!

  - Paul



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