[BioC] hyperGTest, KEGG

[ivan.borozan at utoronto.ca]

Hi,

I've used the script below to calculate over-represented KEGG  
categories however I can not get to gene ID's associated with each of  
the overrepresented KEGG terms/pathways ?

hgCutoff <- 0.01
  params <- new("KEGGHyperGParams", geneIds = selectedEntrezIds,  
universeGeneIds = entrezUniverse, annotation = "Hu19K8Build17102006",   
pvalueCutoff= hgCutoff, testDirection = "over")
hgOver <- hyperGTest(params)


summary(hgOver)

gives

   KEGGID       Pvalue OddsRatio  ExpCount Count Size
1  04360 3.197873e-05 11.175439 1.0410959     5   19
2  05214 6.071664e-04  7.510345 1.1506849     7   21
3  01030 2.025983e-03 10.447619 0.6027397     3   11


however if I do

> catToGeneId(hgOver)
Error: could not find function "catToGeneId"

My question, does catToGeneId() exist and how do I get to genes that  
are associated with each of the above pathways ?

all the best,
Ivan

R version 2.4.0 (2006-10-03)

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
[7] "utils"     "datasets"  "base"

other attached packages:
Hu19K8Build17102006             GOstats            Category           
genefilter
             "1.1.0"             "2.0.4"             "2.0.3"            
  "1.12.0"
                KEGG                RBGL                  GO            
     graph
            "1.14.1"            "1.10.0"            "1.14.0"            
  "1.12.0"
            siggenes            multtest            survival            
  annotate
             "1.8.0"            "1.12.0"              "2.29"            
  "1.12.0"
                      Biobase
                      "1.12.1"