Wondering, Is it too off the beaten track to expect
`mcols<-`(x,NULL) 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
