The in-line usage makes sense. How about dropmcols() or something, at least
for removing the mcols?
On Mon, May 5, 2014 at 1:25 AM, Julian Gehring <julian.gehr...@embl.de>wrote:
> 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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