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

[Johnston, Jeffrey]

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
})