[BioC] How to get genes within a GO category of 'GOstat' results?
Atul
atulkakrana at outlook.com
Tue Sep 9 19:31:35 CEST 2014
Hi All,
I am using 'GoStat' package for GO enrichment analysis and so far I have
been able to generate results from 'hyperGTest' without any issue. Here
is my dummy code:
top.genes = read.delim("Top200_others.txt")
## Test set ###########
entrezTest.AF = top.genes[[1]] ## ENTREZ IDs
## Background set #######
all.genes = keys(org.Mm.eg.db, keytype="SYMBOL");all.genes[1:5] ## Using
all genes as background
entrezUniverse.AF = select(org.Mm.eg.db,as.character(all.genes),columns
= "ENTREZID",keytype = "SYMBOL")
b = entrezUniverse.AF[[2]] ## Select the Entrez ids
b <- b[!is.na(b)];length(b)
## Perform Test ##########
hgCutoff <- 0.005
params <-
new("GOHyperGParams",geneIds=entrezTest.AF,universeGeneIds=b,annotation="org.Mm.eg.db",ontology="BP",pvalueCutoff=hgCutoff,conditional=FALSE,testDirection="over")
paramsCond <- params
conditional(paramsCond) <- TRUE
hgOver <- hyperGTest(params)
## Write Results ########
htmlReport(hgOver, file=paste("IL_Mand_RClustGO2",".html",sep=""))
Now all I need is the list of test genes under enriched go categories.
For Ex:
GOBPID Pvalue OddsRatio ExpCount Count Size Term
GO:0009888 0.000 5.988 9 41 1449 tissue development
GO:0009887 0.000 7.597 5 30 789 organ morphogenesis
Which test genes (entrez ids) were present in 'tissue developemnt'? Is
is possible?
Thanks in Advance
AK
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