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
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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P.O. Box 19024
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