[BioC] GOstats and KEGG

[Morten Mattingsdal]

Hi Jim,
Aha... I just replaced GOHyperGParams with KEGGHyperGParams as you told 
me, and then it worked.

 >all_entrez=lookUp(universe,"hgu133plus2","ENTREZID")
 >my_entrez=lookUp(probe,"hgu133plus2","ENTREZID")
 >hgCutoff <- 0.01
 >params <- new("KEGGHyperGParams", geneIds = my_entrez, universeGeneIds 
= all_entrez, annotation = "hgu133plus2",  pvalueCutoff= hgCutoff, 
testDirection = "over")
 >over_kegg<- hyperGTest(params)
Gene to KEGG Category Test for over Representation Test Result
100 KEGG ids tested (3 have p < 0.01)
Selected gene set size: 99
    Gene universe size: 2137
    Annotation package: hgu133plus2

But when I try to write a html report I get the error,

 >htmlReport(over_kegg, file = "KEGG.html")
Error in function (classes, fdef, mtable)  :
        unable to find an inherited method for function "htmlReport", 
for signature "HyperGResult"

any hints how to display the results ? (since Im quite lost by now)

with:
R version 2.4.0
GOstats 2.0.2
annotate: 1.12.0

greatly appreciate any help
morten



James W. MacDonald wrote:
> 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
>
>