[Bioc-devel] GenomicRanges List subclass and apply
Hi Michael, Mostly for sending each element of the GRanges object to a custom function that runs an identical analysis on each element. I have some functions that take as input a single range -> calculate number of reads that overlap the range -> subset the range into K number of segments based on coverage patterns across the range. Thanks! Jack
Michael Lawrence wrote:
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[1], gr[1:2] still works normally.
Are there any recommendations on a workaround for this issue without
resorting back to for loops?
Thanks all,
Jack
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