Entering edit mode
Hi Cl?mentine,
The "db" just adds a ".db" suffix to load the library. Just try
paste(yourDb, "db", sep="."). This will give "yourDb.db". Maybe a
short example will help. There is a list of 8 probesets from tha affy
rat 230 2.0 array. I'm looking which of these transcripts are involved
in the KEGG pathways 04710 (circadian rhythm) and 00240 (Pyrimidine
metabolism):
Regards, Mike
> genelist=c("1368303_at", "1378745_at", "1392640_at", "1369996_at",
+????????????? "1370295_at", "1378180_at", "1388182_at",
"1398875_at")
> KEGGID=c("04710", "00240")
> db="rat2302" #which will load rat2302.db annotation package
>
> myKEGG = KEGG2symbol(KEGGID, genelist, db)
> myKEGG
$`04710`
???????????????????????? [,1]
1368303_at "Per2"
1378745_at "Per3"
1392640_at "Cry1"
$`00240`
????????????????????????? [,1]
1369996_at "Polr2f"
1370295_at "Nme1"
1378180_at "Dctd"
1388182_at "Prim1"
1398875_at "Polr3k"
-----Urspr?ngliche Nachricht-----
Von: "Cl?mentine Dressaire" <clementinedressaire at="" itqb.unl.pt="">
Gesendet: 29.10.2010 15:21:33
An: "Mike Walter" <michael_walter at="" email.de="">
Betreff: Re: [BioC] retrieve genes names after KEGG hypergeometric
test
>
>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,
>
>
>
>Cl?mentine
>
>
>
>
>
>On Fri, 29 Oct 2010 14:23:00 +0200 (CEST), "Mike Walter"
>
><michael_walter at="" email.de=""> wrote:
>
>> Hi Cl?mentine,
>
>>
>
>> 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
>
>>
>
>> -----Urspr?ngliche Nachricht-----
>
>> Von: "Cl?mentine 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.
>
>>>
>
>>>
>
>>>
>
>>>Cl?mentine
>
>>>
>
>>>
>
>>>
>
>>>--
>
>>>
>
>>>Cl?mentine Dressaire
>
>>>
>
>>>Post-doctoral research fellow
>
>>>
>
>>>Control of gene expression lab
>
>>>
>
>>>ITQB - Instituto de Tecnologia Qu?mica e Biol?gica
>
>>>
>
>>>Apartado 127, Av. da Rep?blica
>
>>>
>
>>>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:
>
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