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 <hpa...@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]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> > -- > 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: hpa...@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]]
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