Yes, Look here at what Marc suggested me: http://article.gmane.org/gmane.science.biology.informatics.conductor/4 7912/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/Annotati onDbi/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 >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> 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 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 <http: www.cibiv.at=""> [[alternative HTML version deleted]]