Hi Tim,
I was looking for a similar function a while ago, and created the
'grangesPlain' function in 'SomaticSignatures':
grangesPlain <-
function (x)
{
mcols(x) = NULL
x = as(x, "GRanges")
return(x)
}
It removes the metadata columns, as Michael described. Further, it
performs an explicit conversion to a 'GRanges' object - in case that 'x'
has a derived class like a 'VRanges'.
The main motivation for an extra function is that you can use it inline, e.g
resize(sort(grangesPlain(x)), ...)
works. It would be great to have such functionality as part of the bioc
core.
Best wishes
Julian
On 05.05.2014 01:56, Michael Lawrence wrote:
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.tri...@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" <j...@stowers.org> wrote:
On May 4, 2014, at 3:50 PM, Tim Triche, Jr. <tim.tri...@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
})
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