[Bioc-devel] GenomicRanges List subclass and apply
jfu14 @ending from jhu@edu
Tue May 15 01:07:00 CEST 2018
Thanks all -> I definitely see the appeal of vectorization.
I'm going to take a few pokes to do just that.
Hervé Pagès wrote:
> Hi Jack,
> You can use
> sapply(seq_along(gr), function(i) print(gr[i]))
> instead of
> sapply(gr, print)
> But yes, as Michael noted, looping on a GRanges or IRanges object
> is generally not efficient and should be avoided. There is almost
> always a "vectorized" solution and it's generally much faster.
> However, depending on what you are trying to do exactly, coming up
> with a "vectorized" solution can be tricky.
> On 05/14/2018 07:28 AM, Jack Fu wrote:
>> Hey all,
>> I think some of the recent changes to GRanges has affected using the
>> apply class functions with GRanges objects:
>> o GenomicRanges now is a List subclass. This means that GRanges
>> and their derivatives are now considered list-like objects
>> (even though
>> [[ don't work on them yet, this will be implemented in
>> Bioconductor 3.8).
>> The following code will throw:
>> gr <- GRanges(1, IRanges(1:2, 3:4))
>> sapply(gr, print)
>> Error in (function (classes, fdef, mtable) :
>> unable to find an inherited method for function 'getListElement' for
>> signature '"GRanges"'
>> Access using gr, gr[1:2] still works normally.
>> Are there any recommendations on a workaround for this issue without
>> resorting back to for loops?
>> Thanks all,
>> [[alternative HTML version deleted]]
>> Bioc-devel at r-project.org mailing list
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