[BioC] html report of hyperGTest question

[Siarhei Manakou]

Hello,

I was testing over-representation  of  GO categories and generating nice 
HTML reports through these commands:

 >params<-new("GOHyperGParams",
 >geneIds=genelist1UQ,
 >universeGeneIds=EntrezUniverse,
 >annotation="mouse4302",
 >ontology="BP",
 >pvalueCutoff=0.001,
 >conditional=FALSE,
 >testDirection="over")
 >GOover<-hyperGTest(params)
 >htmlReport(GOover, file="GO_MCL_cluster1")

However, when i tried to do similar for KEGG pathways and PFAM domains 
through the following:

KEGG:
 >params<-new("KEGGHyperGParams",
 >geneIds=genelist1UQ,
 >universeGeneIds=EntrezUniverse,
 >annotation="mouse4302",
 >pvalueCutoff=0.001,
 >testDirection="over")
 >keggOver<-hyperGTest(params)
 >htmlReport(keggOver, file="GO_MCL_cluster1")

PFAM:
 >params<-new("PFAMHyperGParams",
 >geneIds=genelist1UQ,
 >universeGeneIds=EntrezUniverse,
 >annotation="mouse4302",
 >pvalueCutoff=0.001,
 >testDirection="over")
 >pfamOver<-hyperGTest(params)
 >htmlReport(pfamOver, file="GO_MCL_cluster1")

-the "problem" with these reports is:
1)unlike in GO report there is no "Term" column  which human can 
understand, and only KEGG/PFAM ids are listed
2)to make things worse - there is no html links from these ids, and to 
see what are the things i have to paste them individually into the 
google etc.

So is there an easy way to add links to the descriptive column to the 
HTML reports  and to add HTML links to them?

Thanks a lot!
Sergei



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