Done. (see Coercion section in ?GRanges) Thanks for trusting the professionals.
H. On 09/15/2015 10:51 AM, Tim Triche, Jr. wrote:
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 <mailto: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> <mailto: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> <mailto: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>> >> <mailto: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>>> >> <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: >> >> 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>>>> >> <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 <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>>>> >> <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 <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>> >> >> >> <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 <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>>>> >> <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 <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> >> <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> >> <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>> >> >> >> <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 <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> >> >> >> >> -- >> 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> > [[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>> 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
