Hi Michael, We decided to come up with one function called keepStandardChromosomes() which is a wrapper for both the functions suggested by you (i.e., keepPrimaryChromosomes() and keepAutosomes() ) Here is an example: library(AnnotationDbi) library(GenomicRanges) txdb <- loadDb(system.file("extdata", "UCSC_knownGene_sample.sqlite", package="GenomicFeatures")) trans <- transcripts(txdb) seqlevels(trans) #gets all GRanges for Human chromosomes : 1-22,X,Y,M got <- keepStandardChromosomes(trans,style="UCSC", species="Homo sapiens") seqlevels(got) #for getting only autosomes, one could then extract using keepSeqlevels() #as shown earlier: keepSeqlevels(got,c("chrX","chrY")) keepSeqlevels(got,c("chrX","chrY", "chrM")) Thanks and Regards Sonali. On 12/25/2013 4:15 AM, Michael Lawrence wrote: > Awesome -- how about keepAutosomes? > > > On Tue, Dec 24, 2013 at 1:11 PM, Arora, Sonali > wrote: > > Hi everyone, > > We are pleased to announce that we have added a new function called > keepStandardChromosomes() to GenomicRanges(1.15.18) - devel branch. > > This function allows a user to subset a given object (containing a > seqinfo class) to > retain only the primary chromosomes and the autosomes. > > Please feel free to get back if you face any issues. > > Thanks, > Sonali Arora. > > On 12/16/2013 11:01 AM, Michael Lawrence wrote: >> Awesome, thanks, Sonali. And welcome to the team. >> >> Michael >> >> >> On Mon, Dec 16, 2013 at 10:38 AM, Arora, Sonali > > wrote: >> >> Hi Michael, >> >> That is an extremely interesting question. We have a couple >> of ideas and are beginning to work on it. >> We hope to come up with something soon. >> >> Thanks, >> Sonali. >> >> >> On 12/16/2013 6:14 AM, Michael Lawrence wrote: >> >> should be stored with the Seqinfo. It could be imputed >> (along with the isCircular I think) via th >> >> >> _______________________________________________ >> Bioc-devel@r-project.org >> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> > > [[alternative HTML version deleted]]