Hi Jack,
You can use
sapply(seq_along(gr), function(i) print(gr[i]))
instead of
sapply(gr, print)
But yes, as Michael noted, looping on a GRanges or IRanges object
is generally not efficient and should be avoided. There is almost
always a "vectorized" solution and it's generally much faster.
However, depending on what you are trying to do exactly, coming up
with a "vectorized" solution can be tricky.
Cheers,
H.
On 05/14/2018 07:28 AM, Jack Fu 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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