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, Herv? Pag?s <hpages at fredhutch.org>
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")
?
~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
--
Herv? Pag?s
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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