[BioC] GO.db and Gostats question

[Marc Carlson]

Hi Adi,

In addition to the gene list you provide, and the GO DAG, there is also
information (from the annotation package that you specify) to indicate
which GO terms should be associated with which gene IDs. 

  Marc




Tarca, Adi wrote:
> Hi all,
>
> I have a question regarding the way in which GOstats scans the GO tree and counts how many genes in a given list belong to those go terms.
> Here is how I would look for all BP GO terms that have one or more genes in a given list called ALL:     
>
> library(org.Hs.eg.db)
> library(GO.db)
> ALL=c("6462","54784","386678","1572","57830","51764","85443","387644","54807","401106","11012","26529")
> xyy<- as.list(org.Hs.egGO2ALLEGS)
> x1 <- as.list(GOTERM)
> alGO=names(xyy)
> out<-list()
> for (i in 1:length(alGO)){
> mygo=alGO[i]
> if(Ontology(x1[[mygo]])=="BP"){
> genesgo=intersect(as.vector(xyy[[mygo]]),ALL)
> out[[i]]<-genesgo
> }
> }
> table(unlist(lapply(out,length)))
>
>
> I am not concerned here with the speed of the process by merely finding the same BP terms that GOstats would find. I see that hyperGTest uses both an universeGeneIds argument but also an annotation argument, and I am not sure why the annotation argument is needed given that the universeGeneIds is provided.
> Note that I can not get the list of all terms tested by GOstats using something like:
>
> library(GOstats)
> params <- new("GOHyperGParams", geneIds = ALL,
>  universeGeneIds = ALL, annotation = "hgu133plus2.db",
>  ontology = "BP", pvalueCutoff = 1, conditional = FALSE,
>  testDirection = "over")
> hgCondOver <- hyperGTest(params)
>
> Because all p values will be exactly 1, hyperGTest will return no entries since none are less than the pvalueCutoff. 
>
>
>
>
> Thanks a lot,
>
> Adi 
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