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

[Hector Corrada Bravo]

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
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> Fax:    (206) 667-1319
>
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