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

[Julian Gehring]

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.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
>>> })
>>>
>>>
>>>
>>
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>>
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