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