Dear James, Thank you. This works brilliantly. However it now returns ENSG ids (previously entrez IDs). When I try to map these into gene symbols using og.Hs.egENSEMBL, about 20% of ENSG ids are not found. Should I use another database/package to do this conversion? On Fri, Oct 18, 2013 at 2:27 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Adai, > > See makeTranscriptDbFromBiomart() in the GenomicFeatures package. > > Best, > > Jim > > > > > On Friday, October 18, 2013 9:18:46 AM, Adaikalavan Ramasamy wrote: > >> Hi there, >> >> I am using the R package TxDb.Hsapiens.UCSC.hg19.**knownGene to annotate >> SNPs >> using the locateVariants() function from the VariantAnnotation package. >> >> For reasons of compatibility with other pipelines I developed, I would >> like >> to use Ensembl/Gencode annotation. Is there a package for this? Otherwise >> please advice on how best to generate this myself. >> >> Thank you. >> >> Regards, Adai >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > [[alternative HTML version deleted]]