+1 I was in need of this function yesterday and generally about once a week, when looking up ranges in IGV or UCSC.
On Tue, Sep 15, 2015 at 12:59 PM, Michael Lawrence < lawrence.mich...@gene.com> wrote: > Did this as.character method ever get added? It was a good idea, and we > should add it even though we haven't figured out the table stuff yet. It's > fine if it appends the strand whenever there is at least one range with > +/-. > > Michael > > On Mon, Apr 27, 2015 at 2:23 PM, Hervé Pagès <hpa...@fredhutch.org> wrote: > > > On 04/27/2015 02:15 PM, Michael Lawrence wrote: > > > >> It would be nice to have a single function call that would hide these > >> details. It could probably be made more efficient also by avoiding > >> multiple matching, unnecessary revmap lists, etc. tableAsGRanges() is > >> not a good name but it conveys what I mean (does that make it actually > >> good?). > >> > > > > There is nothing specific to GRanges here. We're just reporting the > > frequency of unique elements in a metadata column so this belongs to > > the "extended" Vector API in the same way that findMatches/countMatches > > do. > > > > H. > > > > > >> On Mon, Apr 27, 2015 at 12:23 PM, Hervé Pagès <hpa...@fredhutch.org > >> <mailto:hpa...@fredhutch.org>> wrote: > >> > >> On 04/24/2015 11:41 AM, Michael Lawrence wrote: > >> > >> 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? > >> > >> > >> This was actually the motivating use case for introducing > >> findMatches/countMatches a couple of years ago: > >> > >> ux <- unique(x) > >> mcols(ux)$Freq <- countMatches(ux, x) > >> > >> Don't know what a good API would be to make this even more > >> straightforward though. Maybe via some extra argument to unique() > >> e.g. 'with.freq'? This is kind of similar to the 'with.revmap' > >> argument of reduce(). Note that unique() could also support the > >> 'with.revmap' arg. Once it does, the 'with.freq' arg can also > >> be implemented by just calling elementLengths() on the "revmap" > >> metadata column. > >> > >> H. > >> > >> > >> On Fri, Apr 24, 2015 at 10:54 AM, Hervé Pagès > >> <hpa...@fredhutch.org <mailto:hpa...@fredhutch.org> > >> <mailto:hpa...@fredhutch.org <mailto: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> > >> <mailto:hpa...@fredhutch.org <mailto:hpa...@fredhutch.org>> > >> <mailto:hpa...@fredhutch.org > >> <mailto:hpa...@fredhutch.org> <mailto: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> > >> <mailto:phave...@gene.com <mailto:phave...@gene.com>> > >> <mailto:phave...@gene.com <mailto:phave...@gene.com> > >> <mailto:phave...@gene.com <mailto:phave...@gene.com>>> > >> > >> [[alternative HTML version deleted]] > >> > >> > _______________________________________________ > >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> > >> <mailto:Bioc-devel@r-project.org <mailto: > Bioc-devel@r-project.org > >> >> > >> <mailto:Bioc-devel@r-project.org > >> <mailto:Bioc-devel@r-project.org> > >> <mailto: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> <mailto:hpa...@fredhutch.org > >> <mailto:hpa...@fredhutch.org>> > >> <mailto:hpa...@fredhutch.org > >> <mailto:hpa...@fredhutch.org> <mailto:hpa...@fredhutch.org > >> <mailto:hpa...@fredhutch.org>>> > >> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> > >> <tel:%28206%29%20667-5791> > >> <tel:%28206%29%20667-5791> > >> Fax: (206) 667-1319 <tel:%28206%29%20667-1319> > >> <tel:%28206%29%20667-1319> > >> <tel:%28206%29%20667-1319> > >> > >> > >> _______________________________________________ > >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> > >> <mailto:Bioc-devel@r-project.org <mailto: > Bioc-devel@r-project.org > >> >> > >> <mailto:Bioc-devel@r-project.org > >> <mailto:Bioc-devel@r-project.org> > >> <mailto: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> > >> <mailto:hpa...@fredhutch.org <mailto:hpa...@fredhutch.org>> > >> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> > >> <tel:%28206%29%20667-5791> > >> Fax: (206) 667-1319 <tel:%28206%29%20667-1319> > >> <tel:%28206%29%20667-1319> > >> > >> > >> > >> -- > >> 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> > >> > >> > >> > > -- > > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
