[Bioc-devel] GenomicRanges List subclass and apply

Jack Fu jfu14 @ending from jhu@edu
Mon May 14 16:28:26 CEST 2018

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,

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