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

[Tim Triche, Jr.]

how about:
foo <- paintBikeShed("mauve")  ## :-D

more serious-like, though,

genome(gr) <- "hg19" ## and
gr <- standardizeGenome(gr, "hg19")

seem like the apotheosis of clarity and thus the way to go.



Statistics is the grammar of science.
Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>

On Fri, Jun 5, 2015 at 1:49 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
>

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