[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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