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

[Tim Triche, Jr.]

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
> })
> 
> 
>