Taking this a bit off topic but it would be nice if we could get the GRanges equivalent of as.data.frame(table(x)), i.e., unique(x) with a count mcol. Should be easy to support but what should the API be like?
On Fri, Apr 24, 2015 at 10:54 AM, Hervé Pagès <hpa...@fredhutch.org> wrote: > On 04/24/2015 10:18 AM, Michael Lawrence wrote: > >> It is a great idea, but I'm not sure I would use it to implement >> table(). Allocating those strings will be costly. Don't we already have >> the 4-way int hash? Of course, my intuition might be completely off here. >> > > It does use the 4-way int hash internally. as.character() is only used > at the very-end to stick the names on the returned table object. > > H. > > >> >> On Fri, Apr 24, 2015 at 9:59 AM, Hervé Pagès <hpa...@fredhutch.org >> <mailto:hpa...@fredhutch.org>> wrote: >> >> Hi Pete, >> >> Excellent idea. That will make things like table() work out-of-the-box >> on GenomicRanges objects. I'll add that. >> >> Thanks, >> H. >> >> >> >> On 04/24/2015 09:43 AM, Peter Haverty wrote: >> >> Would people be interested in having this: >> >> setMethod("as.character", "GenomicRanges", >> function(x) { >> paste0(seqnames(x), ":", start(x), "-", end(x)) >> }) >> >> ? >> >> I find myself doing that a lot to make unique names or for >> output that >> goes to collaborators. I suppose we might want to tack on the >> strand if it >> isn't "*". I have some code for going the other direction too, >> if there is >> interest. >> >> >> >> Pete >> >> ____________________ >> Peter M. Haverty, Ph.D. >> Genentech, Inc. >> phave...@gene.com <mailto:phave...@gene.com> >> >> [[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 >> >> >> -- >> 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...@fredhutch.org <mailto:hpa...@fredhutch.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 >> >> >> > -- > 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...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
