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@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
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>
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