rad, I was just about to say, "hey, I've written that function in 3 different places, I think I could send in a patch..." and then of course Herve is on it.
I need to remember to leave things to the professionals... --t On Tue, Sep 15, 2015 at 10:38 AM, Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi Michael and Michael, > > It's on its way. Probably before the end of the week. Thanks for the > reminder! > > H. > > On 09/15/2015 10:07 AM, Michael Love wrote: > >> +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 <mailto: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 >> <mailto: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> >> >> <mailto: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>> >> >> <mailto: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>>> >> >> <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 >> <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>>> >> >> <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 <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> >> >> >> >> >> <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 >> <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 >> >>> >> >> <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 >> <mailto:hpa...@fredhutch.org>>>> >> >> Phone: (206) 667-5791 >> <tel:%28206%29%20667-5791> <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> >> >> <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> >> >> >> >> >> <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 >> <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> >> >> >> >> >> >> >> >> -- >> >> 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> >> > >> >> [[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 > 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]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
