[Bioc-devel] ordering GenomicRanges without regard for strand
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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