[Bioc-devel] ordering GenomicRanges without regard for strand

[Hervé Pagès]

OK. Let's go for unstrand() too. Will add this in the next few days.

H.


On 12/12/2013 05:07 PM, Kasper Daniel Hansen wrote:
> we should have the argument for sort, but I also find unstrand() to be a
> great idea.
>
>
> On Thu, Dec 12, 2013 at 7:19 PM, Hervé Pagès <hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>> wrote:
>
>     Hi Michael,
>
>     Feels like Christmas is not far away ;-)
>
>     Right now only the "match" method in the GenomicRanges-comparison.R
>     family supports the 'ignore.strand' arg and I think it would be a good
>     thing to have other "comparison" methods support it. It's too bad
>     for order() though (but maybe there is a way to hack the definition of
>     the generic in BiocGeneric?). Should be easy for sort(). Will do.
>
>     Cheers,
>     H.
>
>
>
>     On 12/12/2013 01:44 PM, Michael Lawrence wrote:
>
>         It is very common to want to order a GenomicRanges by *position*
>         but not
>         strand. Would be nice to have an ignore.strand argument for ordering
>         GenomicRanges. I realize that this is not possible by the order
>         generic.
>         But it would be possible for sort().
>
>         I also realize that someone could do this:
>
>         gr2 <- gr
>         strand(gr2) <- "*"
>         gr[order(gr2)]
>
>         But that is long-winded. Perhaps there could be an unstrand()?
>
>         gr[order(unstrand(gr))]
>
>         But this is still better:
>
>         sort(gr, ignore.strand=TRUE)
>
>         Sound like a good thing?
>
>         Michael
>
>                  [[alternative HTML version deleted]]
>
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>
>     --
>     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
>
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-- 
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 fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319