Hector: we still need genome version in whatever call we make. I assume we will get an update when this has been implemented; I am itching to use it.
Kasper On Fri, Jun 5, 2015 at 5:04 PM, Michael Lawrence <lawrence.mich...@gene.com> wrote: > That's already possible, basically: > > seqinfo(gr) <- seqinfo(Mus.musculus) > > Anyway, I'm with Tim's last suggestion. Just support both. Have an > argument to genome<- like standardize=FALSE for low-level > manipulation. > > > On Fri, Jun 5, 2015 at 1:56 PM, Hector Corrada Bravo <hcorr...@gmail.com> > wrote: > > Sorry if I'm too late for this... > > > > I think having "hg19" in 'gr <- standardizeSeqinfo(gr, "hg19")' be > > responsible for so much, can make this new function hard to maintain. > > Might it be better if that argument takes an object corresponding to a > > canonical annotation? E.g., > > > > > > library(Mus.musculus) > > gr <- standardizeSeqinfo(gr, Mus.musculus) > > > > > > On Fri, Jun 5, 2015 at 4:49 PM, Hervé Pagès <hpa...@fredhutch.org> > wrote: > >> > >> On 06/05/2015 01:48 PM, Gabe Becker wrote: > >>> > >>> I dunno, standardizeSeqInfo just seems really long for a function name > >>> users are going to have to call. > >>> > >>> At the risk of annoying Herve further, what about > >>> > >>> gr <- castSeqInfo(gr, "gh19") > >> > >> > >> grrrrr! > >> > >>> > >>> ? > >>> > >>> ~G > >>> > >>> On Fri, Jun 5, 2015 at 1:46 PM, Tim Triche, Jr. <tim.tri...@gmail.com > >>> <mailto:tim.tri...@gmail.com>> wrote: > >>> > >>> maybe standardizeSeqinfo or fixSeqinfo is clearer after all > >>> > >>> Statistics is the grammar of science. > >>> Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science> > >>> > >>> On Fri, Jun 5, 2015 at 1:41 PM, Gabe Becker <becker.g...@gene.com > >>> <mailto:becker.g...@gene.com>> wrote: > >>> > >>> > >>> > >>> On Fri, Jun 5, 2015 at 1:39 PM, Tim Triche, Jr. > >>> <tim.tri...@gmail.com <mailto:tim.tri...@gmail.com>> wrote: > >>> > >>> how about just > >>> > >>> gr <- addSeqinfo(gr, "hg19") > >>> > >>> > >>> Add sounds like it's, well, adding rather than replacing (Which > >>> it sometimes would do. > >>> > >>> gr <- fixSeqInfo(gr, "hg19") > >>> > >>> instead? > >>> > >>> ~G > >>> > >>> > >>> -- > >>> Gabriel Becker, Ph.D > >>> Computational Biologist > >>> Genentech Research > >>> > >>> > >>> > >>> > >>> > >>> -- > >>> Gabriel Becker, Ph.D > >>> Computational Biologist > >>> Genentech Research > >> > >> > >> -- > >> Hervé Pagès > >> > >> Program in Computational Biology > >> Division of Public Health Sciences > >> Fred Hutchinson Cancer Research Center > >> 1100 Fairview Ave. N, M1-B514 > >> P.O. Box 19024 > >> Seattle, WA 98109-1024 > >> > >> E-mail: hpa...@fredhutch.org > >> Phone: (206) 667-5791 > >> Fax: (206) 667-1319 > >> > >> _______________________________________________ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > _______________________________________________ > 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
