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! :) > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > 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) Campus Vienna Biocenter 5 (VBC5), Ebene 1, Room 1812.2 Dr. Bohr Gasse 9 A-1030 Wien, Austria Phone: ++43 +1 / 42772-4030 Fax: ++43 +1 / 42772-4098 email: stefanie.tauber@univie.ac.at www.cibiv.at [[alternative HTML version deleted]]