Hi Julian,

What sort of operations need to be implemented this way? I'm usually able
to avoid them somehow. As a last resort, reducing the complexity of the
object helps. For example, you could operate over ranges(gr) if all you
need are the starts and ends.

Michael


On Thu, May 22, 2014 at 5:56 AM, Julian Gehring <julian.gehring@embl.de>wrote:

> Hi,
>
> Is there a fast way of looping over/extracting the entries of a 'GRanges'
> object individually?  Due to the complex structure of a GRanges object, a
> simple solution like
>
> library(GenomicRanges)
> n = 1e4
> gr = GRanges(1, IRanges(1:n, width = 1))
>
> for(i in seq_along(gr)) {
>     x = gr[i]
>     ## more complex code acting on 'x'
> }
>
> takes notably long.  Converting to a 'GRangesList' or 'GenomicRangesList'
> does obviously not improve the situation.  I was wondering if there is some
> dedicated functionality which would allow this in a faster manner, in cases
> where simple vectorized operations are not applicable.
>
> Best wishes
> Julian
>
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