[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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