>On 05/05/2014 01:00 PM, Cook, Malcolm wrote: >> Wondering, >> >> Is it too off the beaten track to expect >> >> `mcols<-`(x,NULL) > > > args(`mcols<-`) > function (x, ..., value) > >Arguments after the ellipsis must be named: > > `mcols<-`(x, value=NULL)
Herve - Great - of course - so - does this not provide the means requested by the original poster? > >Nothing we can do about this. > >Cheers, >H. > >> >> to work? >> >> hint: it does not >> >> >-----Original Message----- >> >From: bioc-devel-boun...@r-project.org >> [mailto:bioc-devel-boun...@r-project.org] On Behalf Of Hervé Pagès >> >Sent: Monday, May 05, 2014 1:28 PM >> >To: Kasper Daniel Hansen; Michael Lawrence >> >Cc: Johnston, Jeffrey; ttri...@usc.edu; bioc-devel@r-project.org; >> bioconduc...@r-project.org >> >Subject: Re: [Bioc-devel] [BioC] granges() method for GenomicRanges >> objects akin to ranges()... >> > >> >Hi, >> > >> >I have no problem using granges() for that. Just to clarify: >> > (a) it would propagate the names() >> > (b) it would drop the metadata() >> > (c) the mcols() would propagate only if 'use.mcols=TRUE' was >> > specified ('use.mcols' is FALSE by default) >> > (d) it would return a GRanges *instance* i.e. input object 'x' >> > would be downgraded to GRanges if it extends GRanges >> > >> >@Kasper: granges() on SummarizedExperiment ignores the 'use.mcols' >> >arg and always propagates the mcols. Alternatively you can use rowData() >> >which also propagates the mcols. granges() is actually just an alias >> >for rowData() on SummarizedExperiment objects. >> > >> >H. >> > >> > >> >On 05/05/2014 10:31 AM, Kasper Daniel Hansen wrote: >> >> I agree with Michael on this. >> >> >> >> I can see why, in some usage cases, granges() is convenient to have >> with >> >> use.mcols=FALSE (which seems to have been added in the latest release). >> >> But in my usage of granges(), where I call granges() on objects like >> >> SummarizedExperiments and friends, I have been expecting granges() to >> give >> >> me the GRange component of the object. Not a crippled version of the >> >> GRange component. >> >> >> >> This is - to me - very counter intuitive and I wish I had seen this >> >> earlier. It is particular frustrating that this default is part of the >> >> generic. >> >> >> >> Best, >> >> Kasper >> >> >> >> >> >> On Mon, May 5, 2014 at 12:11 PM, Michael Lawrence >> <lawrence.mich...@gene.com >> >>> wrote: >> >> >> >>> In my opinion, granges() is not very clear as to the intent. The >> mcols are >> >>> part of the GRanges, so why would calling granges() drop them? I >> think we >> >>> want something similar to unclass(), unname(), etc. This why I >> suggested >> >>> dropmcols(). >> >>> >> >>> >> >>> >> >>> >> >>> On Mon, May 5, 2014 at 8:17 AM, Tim Triche, Jr. <tim.tri...@gmail.com >> >>>> wrote: >> >>> >> >>>> That's exactly what I was after -- the generic is already defined, >> so why >> >>>> not use it? >> >>>> >> >>>> --t >> >>>> >> >>>>> On May 5, 2014, at 7:42 AM, Julian Gehring <julian.gehr...@embl.de> >> >>>> wrote: >> >>>>> >> >>>>> Hi, >> >>>>> >> >>>>>> On 05.05.2014 16:22, Martin Morgan wrote: >> >>>>>> generalize as setMcols, like setNames? setMcols(x, NULL) >> >>>>> >> >>>>> How about Tim's original suggestion, to add a 'granges' method that >> >>>> works on a 'GRanges' input? The current definition >> >>>>> >> >>>>> granges(x, use.mcols=FALSE, ...) >> >>>>> >> >>>>> seem suited for this. >> >>>>> >> >>>>> Best wishes >> >>>>> Julian >> >>>> >> >>> >> >>> [[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 >> >> >> > >> >-- >> >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 >> > >-- >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
