Yes,
Look here at what Marc suggested me:
http://article.gmane.org/gmane.science.biology.informatics.conductor/47912/m
atch=borello

Ugo



From: Stefanie Tauber <stefanie.tauber@univie.ac.at>
Date: Mon, 6 May 2013 13:05:31 +0200
To: Ugo Borello <ugo.borello@inserm.fr>
Cc: <bioconductor@stat.math.ethz.ch>
Subject: Re: [BioC] retrieving external Gene IDs from TranscriptDB Object

Thanks for pointing out the vignette.
Definitely helpful.
Probably the way to go is downloading the corresponding org.*.db package and
then use the appropriate keys.
Thanks!


Am 06.05.2013 um 12:18 schrieb Ugo Borello <ugo.borello@inserm.fr>:

> Dear Stefanie,
> I just learned, thanks to Marc Carlson, an easy way to do what you want.
> It is nicely described in this vignette, section 05 (and 03):
> http://www.bioconductor.org/packages/release/bioc/vignettes/AnnotationDbi/in
> st/doc/IntroToAnnotationPackages.pdf
> I hope this help.
> Ugo
> 
> 
>> From: Stefanie Tauber <stefanie.tauber@univie.ac.at>
>> Date: Mon, 6 May 2013 11:25:09 +0200
>> To: <bioconductor@stat.math.ethz.ch>
>> Subject: [BioC] retrieving external Gene IDs from TranscriptDB Object
>> 
>> Dear List,
>> 
>> I have created a TranscriptDB for yeast as follows:
>> 
>> library(GenomicFeatures)
>> library(biomaRt)
>> 
>> ## create yeast DB
>> myDB <- makeTranscriptDbFromBiomart(biomart = "ensembl", dataset =
>> "scerevisiae_gene_ensembl", circ_seqs = c(DEFAULT_CIRC_SEQS, "Mito"))
>> myDBx <- cdsBy(myDB,by = "tx",use.names = TRUE)
>> 
>> Now, I would like to retrieve the external gene ids.
>> Is this the most generic way?
>> 
>> # select mart and dataset
>> mymart = useMart("ENSEMBL_MART_ENSEMBL", dataset =
>> "scerevisiae_gene_ensembl", host="www.ensembl.org")
>> 
>> # just a selection of transcripts
>> 
>> sel = names(myDBx)[5:6]
>> 
>> getBM(attributes=c("ensembl_transcript_id","external_gene_id"), values =
>> sel, filters = "ensembl_transcript_id", mart = mymart)
>> 
>> 
>> And, when creating a TranscriptDB From UCSC:
>> 
>> 
>> myDB1 <- makeTranscriptDbFromUCSC(genome = "hg19",tablename = "knownGene")
>> myDBx1 <- cdsBy(myDB1,by = "tx",use.names =TRUE)
>> 
>> What would be here the most generic way to retrieve the external gene IDs
>> for each transcript ID?
>> 
>> Best,
>> Stefanie
>> 
>> 
>>> sessionInfo()
>> R Under development (unstable) (2013-05-02 r62711)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>> 
>> locale:
>>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>  [7] LC_PAPER=C                 LC_NAME=C
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>> 
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>> [8] base
>> 
>> other attached packages:
>> [1] biomaRt_2.16.0         GenomicFeatures_1.12.1 AnnotationDbi_1.22.3
>> [4] Biobase_2.20.0         GenomicRanges_1.12.2   IRanges_1.18.0
>> [7] BiocGenerics_0.6.0
>> 
>> loaded via a namespace (and not attached):
>>  [1] Biostrings_2.28.0  bitops_1.0-5       BSgenome_1.28.0    DBI_0.2-6
>>  [5] RCurl_1.95-4.1     Rsamtools_1.12.2   RSQLite_0.11.3
>> rtracklayer_1.20.1
>>  [9] stats4_3.1.0       tools_3.1.0        XML_3.96-1.1       zlibbioc_1.6.0
>> 
>> _______________________________________________
>> Bioconductor mailing list
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>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> 

DI Stefanie Tauber

Center for Integrative Bioinformatics Vienna (CIBIV)
(CIBIV is a joint institute of Vienna University and Medical University)
Max F. Perutz Laboratories (MFPL)
Campus Vienna Biocenter 5 (VBC5), Ebene 1, Room 1812.2
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email:   stefanie.tauber@univie.ac.at
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