[BioC] retrieve genes names after KEGG hypergeometric test

[Mike Walter]

Hi Clémentine,

I don't know, if such a function exists. I use two little helper functions to retrieve probe IDs or gene symbols of genes in a genelist, that are associated with a KEGG ID:

KEGG2genes = function(KEGGID, genelist, db){
 require(paste(db, "db", sep="."), character.only = TRUE)
 l = vector("list")
 for (i in 1:length(KEGGID)){
 kegg = as.matrix(unlist(mget(KEGGID[i], get(paste(db, "PATH2PROBE", sep="")), ifnotfound=NA)))
 l[[i]] = genelist[is.element(genelist,kegg[,1])]
 }
names(l)=KEGGID
l
}

KEGG2symbol = function(KEGGID, genelist, db){
 l = vector("list")
 for (i in 1:length(KEGGID)){
 id = unlist(KEGG2genes(KEGGID=KEGGID[i], genelist=genelist, db=db))
 l[[i]] = as.matrix(mget(id, get(paste(db, "SYMBOL", sep="")), ifnotfound=NA))
 }
 names(l)=KEGGID
 l
}

where "KEGGID" is a character vector of your KEGGID(s) you are interested in, "genelist" is a character vector containing the probe IDs/probeset IDs of your genelist you used to create the KEGGHyperGResult and "db" is a character vector with the annotation database for your array without the .db extension (e.g. db="hgu133plus" for the affy U133+ 2.0 array). As a result you get a matrix containing the probeIDs and genesymbols for each KEGGID stored in a list. It might not be the most elegant way, but it works. 

Kind regards, 

Mike

-----Ursprüngliche Nachricht-----
Von: "Clémentine Dressaire" <clementinedressaire at itqb.unl.pt>
Gesendet: 29.10.2010 13:27:44
An: bioconductor at stat.math.ethz.ch
Betreff: [BioC] retrieve genes names after KEGG hypergeometric test

>
>Dear BioC users,
>
>
>
>I performed different hypergometric tests on my data regarding GO terms
>
>and KEGG pathways. With GO resukt I can use the probeSetSummary function to
>
>retrieve the gene list associated to each significant category.
>
>However this function does not work if I apply the HG test using
>
>KEGGHyperGParams because the results are not of GOHyperGResult class... Is
>
>there any equivalent KEGG function to get those genes list? 
>
>
>
>WIth advanced thanks for your help.
>
>
>
>Clémentine 
>
>
>
>-- 
>
>Clémentine Dressaire
>
>Post-doctoral research fellow
>
>Control of gene expression lab
>
>ITQB - Instituto de Tecnologia Química e Biológica
>
>Apartado 127, Av. da República
>
>2780-157 Oeiras
>
>Portugal
>
>+351 214469562
>
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