[BioC] retrieve genes names after KEGG hypergeometric test

[Clémentine Dressaire]

Hi Mike,

 

Could ou explain me the difference between the db and "db" you are using?

If db is the character vector with the annotation database for your array

without the .db extension, then what does db represent?



Again thanks for your help,



Clémentine





On Fri, 29 Oct 2010 14:23:00 +0200 (CEST), "Mike Walter"

<michael_walter at email.de> wrote:

> 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

>>

>>_______________________________________________

>>Bioconductor mailing list

>>Bioconductor at stat.math.ethz.ch

>>https://stat.ethz.ch/mailman/listinfo/bioconductor

>>Search the archives:

>>http://news.gmane.org/gmane.science.biology.informatics.conductor