[BioC] additional to GOHyperG

[Auer Michael]

Only recently I have posted the problem of not having the corresponding
Affy IDS and Locus IDS to the significant nodes from a GOHyperG
application.
I think this is a problem every body encounters sooner or later when
working with gene ontologies.

I have a temporary solution which performs quite well.
So here is the code:
input:
GOLOCmap: This is the result from applying GOALLLOCUSID to the set of
significant GO IDS. Its a list and every element corresponds to a certain
GO ID and the entries to the LOCUS IDS mapping on it.
LOC: This are the AffyIDS and the corresponding LOCUS IDS, a vector. It
comes from applying hgu133aLOCUSID to a set of AffyIDS.

The function looks for the Locus IDS (LOC) in the entries of every element
of the list GOLOCmap.
The result is a list. Every element corresponds to a certain GO ID and the
entries are the ocurring AffyIDS.

Locus_Affy_fromGO<-function(GOLOCmap,LOC)
{
LOCs<-sort(LOC)
maximum<-max(LOCs)
output<-as.list(1:length(names(GOLOCmap)))
res<-0
for (i in 1:length(names(GOLOCmap)))
{
output[[i]]<-list(GOID=names(GOLOCmap)[[i]],LOCUSIDSAffyIDS=c(1,2))

	GOLOCmaps<-sort(GOLOCmap[[i]])
j<-1
while(GOLOCmaps[j]<= maximum)
{
	if(j>=length(GOLOCmaps)) break
res<-c(res,LOCs[LOCs==GOLOCmaps[j]])
j<-j+1
}


output[[i]]$LOCUSIDSAffyIDS <-res[-1]
res<-0
}
output
}


I hope it is useful for some of you. And please let me know if any bugs
are occuring.

Best regards

Michael