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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
