[Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

[Kasper Daniel Hansen]

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.michael at 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 <hcorrada at 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 <hpages at 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.triche at gmail.com
> >>> <mailto:tim.triche at 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.gabe at gene.com
> >>>     <mailto:becker.gabe at gene.com>> wrote:
> >>>
> >>>
> >>>
> >>>         On Fri, Jun 5, 2015 at 1:39 PM, Tim Triche, Jr.
> >>>         <tim.triche at gmail.com <mailto:tim.triche at 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: hpages at fredhutch.org
> >> Phone:  (206) 667-5791
> >> Fax:    (206) 667-1319
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
>
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