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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