[Bioc-devel] ordering GenomicRanges without regard for strand

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, Herv? Pag?s <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

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