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

[Hervé Pagès]

Hi 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)

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