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ivan.borozan@utoronto.ca
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80
@ivanborozanutorontoca-704
Last seen 10.2 years ago
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"