OK. Let's go for unstrand() too. Will add this in the next few days.
H. On 12/12/2013 05:07 PM, Kasper Daniel Hansen wrote:
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 <mailto: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 <mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/__listinfo/bioc-devel <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 <mailto:hpa...@fhcrc.org> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> Fax: (206) 667-1319 <tel:%28206%29%20667-1319> _________________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/__listinfo/bioc-devel <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
