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

Why not just do

mcols(gr) <- NULL

It's way more obvious than granges(gr). And that should happen virtually
instantaneously in R 3.1, regardless of the length.




On Sun, May 4, 2014 at 3:55 PM, Tim Triche, Jr. <tim.triche at gmail.com>wrote:

Right, what I was wondering however is whether it's possible not to create
or modify the object at all, but rather access only the necessary bits.

It seems like a slightly different structure that puts all the location in
one place (say @granges) and the metadata in another (as it presently is)
might be handy to avoid this hoohah.  That's rather a larger change.

--t

On May 4, 2014, at 3:23 PM, "Johnston, Jeffrey" <jjj at stowers.org> wrote:

On May 4, 2014, at 3:50 PM, Tim Triche, Jr. <tim.triche at gmail.com>

wrote:

I wanted something to extract @ranges from a GRanges object along with

its

@seqnames, @strand, and @seqinfo.  Essentially, everything but the

mcols.

Does this make sense?  Is there a lighter-weight way to avoid any

copying

in-flight?


setMethod("granges", "GRanges", function(x) {
         GRanges(seqnames=seqnames(x),
                 ranges=ranges(x),
                 strand=strand(x),
                 seqinfo=seqinfo(x))
})


The fact that I'm constructing an entire new GRanges makes me a little
queasy... that said, it has turned out to be useful when I just want a
short list of locations, as for debugging plotting functions, profile
plots, or what have you.

Perhaps just this:

setMethod("granges", "GRanges", function(x) {
  mcols(x) <- NULL
  x
})

	[[alternative HTML version deleted]]