[Bioc-devel] GenomicRanges List subclass and apply
l@wrence@mich@el @ending from gene@com
Mon May 14 16:49:17 CEST 2018
Just out of curiosity, why are you looping over a GRanges in the first place?
On Mon, May 14, 2018 at 7:28 AM, Jack Fu <jfu14 at jhu.edu> 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 objects
> 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,
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