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

[Michael Lawrence]

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
>>
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>
>