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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Program in Computational Biology
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