[BioC] How to use GOSlim with GOstats

[Marc Carlson]

Hi Iain,

I am a little curious about what you are planning to do with GOSLIM? To
change the annotation used in GOstats, you would normally put the name
of the appropriate annotation package into the annotation slot of the
GOHyperGParams object. But as I am sure you have noticed we don't have
annotation packages for GOSLIM. However, according to the gene ontology
website, a GOSLIM is a subset of the existing GO ontology. So the
appropriate organism package for yeast (which is already based on what
they have at SGD as much as possible) should already provide all the
information you would need for that.


Marc




Iain Wallace wrote:
> Hi all,
>
> I was wondering if somebody could point me in the right direction. I would
> like to use GOSlim from the SGD
> website<ftp://genome-ftp.stanford.edu/pub/yeast/data_download/literature_curation/>with
> the GOStats package, but I am not sure how to change the
> ontology/annotation.
>
> I am currently using the following set of commands to do my Go analysis.
> library(GOstats)
> library("org.Sc.sgd.db")
> x <- org.Sc.sgdGENENAME  #To generate the set of gene names
> mapped_genes <- mappedkeys(x)
> sel<-mapped_genes[1:10]   #selected set of genes
> uni<-mapped_genes           #universe of genes
> params=new("GOHyperGParams",geneIds=sel,universeGeneIds=uni,annotation="org.Sc.sgd.db",ontology="BP",pvalueCutoff=0.05,conditional=FALSE,testDirection="over")
> over=over=hyperGTest(params)
>
> Thanks for any help,
>
> Iain
>
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