This also works,
but addresses the knownGene Table from USCS.
In my code I addressed Ensembl genes with gene status "known".

Which then results in a slightly different selection of genes..


Am 13.06.2012 um 05:31 schrieb Tim Triche, Jr.:

> or just
> 
> biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")
> library("TxDb.Hsapiens.UCSC.hg19.knownGene")
> tx.by.gene <- transcriptsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, 'gene')
> 
> which will be indexed by EntrezGene ID
> Not sure if this is what you were looking for, though.
> 
> 
> 
> On Tue, Jun 12, 2012 at 3:24 AM, Stefanie <stefanie.tauber@univie.ac.at> wrote:
> Hi,
> 
> I just managed to do it the following way:
> 
> I get the transcript IDs of all known genes by the following command:
> 
> ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
> 
> res = getBM(attributes = "ensembl_transcript_id", filters = "status", values =
> "known", mart = ensembl)
> 
> humanDb = makeTranscriptDbFromUCSC(genome = "hg19", tablename =
> "ensGene",transcript_ids = as.character(res[,1]))
> 
> tx = transcriptsBy(humanDb)
> 
> 
> Works! :)
> 
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> 
> 
> 
> -- 
> A model is a lie that helps you see the truth.
> 
> Howard Skipper
> 

DI Stefanie Tauber

Center for Integrative Bioinformatics Vienna (CIBIV)
(CIBIV is a joint institute of Vienna University, Medical University, and University of Veterinary Medicine, Vienna, Austria)
Max F. Perutz Laboratories (MFPL)
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email:   stefanie.tauber@univie.ac.at
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