[BioC] [Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...

[Cook, Malcolm]

>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-bounces at r-project.org [mailto:bioc-devel-bounces at 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; ttriche at usc.edu; bioc-devel at r-project.org; bioconductor at 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.michael at 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.triche at 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.gehring at 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 at r-project.org mailing list
 >>   >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
 >>   >>>
 >>   >>
 >>   >> 	[[alternative HTML version deleted]]
 >>   >>
 >>   >> _______________________________________________
 >>   >> Bioc-devel at 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: hpages at fhcrc.org
 >>   >Phone:  (206) 667-5791
 >>   >Fax:    (206) 667-1319
 >>   >
 >>   >_______________________________________________
 >>   >Bioc-devel at 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: hpages at fhcrc.org
 >Phone:  (206) 667-5791
 >Fax:    (206) 667-1319