Thanks all -> I definitely see the appeal of vectorization.
I'm going to take a few pokes to do just that.
Best,
Jack
Hervé Pagès wrote:
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
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 fast
It's possible that you could vectorize this code. Maybe open an issue
on the support site.
On Mon, May 14, 2018 at 7:56 AM, Jack Fu wrote:
> 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
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
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 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 subcl
