[BioC] How to get genes within a GO category of 'GOstat' results?

[James W. MacDonald]

Hi Atul,

See ?probeSetSummary. You can also use ReportingTools to create a nicer
version of the HTML table you have made, but with links to sub-tables that
contain the significant genes that caused that term to be significant (see
pages 4-5 in the ReportingTools basics vignette
http://bioconductor.org/packages/release/bioc/vignettes/ReportingTools/inst/doc/microarrayAnalysis.pdf
).

Best,

Jim



On Tue, Sep 9, 2014 at 1:31 PM, Atul <atulkakrana at outlook.com> wrote:

> 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
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

	[[alternative HTML version deleted]]