[BioC] GOstats and KEGG

[James W. MacDonald]

Hi Morten,

Morten Mattingsdal wrote:
> Hello everyone,
> 
> Ill be brief:
> I find the updated version of GOstats very useful (version 2.0.2), and I 
> look forward to present the results for the experimentalists. But I also 
> want to do a similar testing with KEGG pathways, where KEGG pathways in 
> my sig. DE list are compared against the "universe" of KEGG pahways on 
> my array.
> 
> hyperGTest only works with GO terms (as it should), but would it be 
> possible to expand it to include KEGG pathways ? If not, what libraries 
> do people use to test for overrepresented pathways in a toplist ?

You are mistaken. hyperGTest() works with any of three input objects; 
GOHyperGParams, KEGGHyperGParams, and PFAMHyperGParams. You instantiate 
a KEGGHyperGParams object the same way as for a GOHyperGParams object 
(only with KEGG ids), and then feed it to hyperGTest().

The help pages for these objects are in the Category package, which may 
be why you missed them.

Best,

Jim


> 
> regards,
> morten
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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