Michael, Since there is no universal seqnameStyle defined for various objects and they do not internally store the seqnameStyle and species information, we decided to ask the user for all 3 arguments. Marc is aware of these issues and my code.
Regarding the dependency of GenomicRanges on AnnotationDbi - Martin was also concerned about this. Both he and Herve are away at the moment - we plan to address this dependency once they get back. Thanks and Regards, Sonali. On 12/27/2013 12:11 PM, Michael Lawrence wrote: > I guess you mean dropSeqlevels, not keepSeqlevels? That should work. > But your function needs some tweaking, I think. The function should > just take the seqnameStyle from the object. There's no need to require > the user to specify it, and then check for consistency. I would like > to be able to just call: > > keepStandardChromosomes(trans) > > Also, I think you made GenomicRanges depend on AnnotationDbi. That's a > major change. Before, it was just in Suggests. Did you discuss this > with anyone? > > Michael > > > > > On Fri, Dec 27, 2013 at 11:37 AM, Arora, Sonali <sar...@fhcrc.org > <mailto:sar...@fhcrc.org>> wrote: > > 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 <sar...@fhcrc.org >> <mailto:sar...@fhcrc.org>> 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 >>> <sar...@fhcrc.org <mailto:sar...@fhcrc.org>> 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 >>> <mailto:Bioc-devel@r-project.org> mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>> >> >> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel