Hi Marc, Thank you for your reply. I was trying to get this done using an older version of R that happened to be running on our cluster, GenomicFeatures has been updated and everything is sorted now. Thanks! Paul. On Thu, Jan 20, 2011 at 11:53 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > Hi Paul, > > If you are using a current enough version of GenomicFeatures then this > will do something like that: > > eaTx <- exonsBy(hgTxDb, 'tx', use.names=TRUE) > > I can't tell if this will help you though since you did not post > sessionInfo(). ?If it doesn't work, then you can also use exons() and > get the data by requesting "tx_name" for the columns argument. > > > ?Marc > > > > On 01/20/2011 11:36 AM, Paul Geeleher wrote: >> Hi, >> >> I've noticed when I use exonsBy() to download exons by transcript like this: >> >> library(GenomicFeatures) >> hgTxDb <- makeTranscriptDbFromUCSC(genome="hg18", tablename="ensGene") >> eTx <- exonsBy(hgTxDb, 'tx') >> >> That the object returned (eTx in this case) doesn't contain the >> transcript names. But if we use >> >> e <- exonsBy(hgTxDb, 'gene') >> >> The ensembl gene names are returned as the names of GRangesList "e". >> I'm wondering if there's a convenient way of annotating the eTx object >> with the transcript names also? >> >> Thanks, >> >> Paul. >> >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Paul Geeleher (PhD Student) School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland -- www.bioinformaticstutorials.com