[Bioc-devel] applying over GRanges and other vectors of ranges

Cook, Malcolm MEC at stowers.org
Mon Sep 24 16:58:37 CEST 2012

> Did you see Malcolm Cook's post recently about fixing pvec() to automatically do this?
> It seems like a sensible approach to me

Thanks Tim, I was poised to chime in...

As Tim said, recently discussed was making pvec work with Lists (including GRangesList) where I offer:

	Here is a (better?) version that does: https://gist.github.com/3757873
	Comments?  Improvements?  Is it better?

I had intended to correspond with parallel author on this matter.  Is that you Michael?

Michael, I think I also have a working version of your sblapply, more or less.

Indeed I would not be surprised if that is what the OP really hope for (guessing here), allowing for a parallel version.

I think I have done it in a way that supports using multicore/parallel and possibly other back ends as Vincent observed is desirable.

I will gist it later today for consideration.

In the meantime, I would appreciate any one to try, criticize, fix, amend my pvec redux (above).



> --t
> On Sep 24, 2012, at 6:53 AM, Michael Lawrence <lawrence.michael at gene.com> wrote:
> > Florian's post about mclapply got me thinking about how it is kind of a
> > pain to iterate over GRanges objects (since they are not Lists, there is no
> > lapply). Could we instead have an apply function for vectors that subsets,
> > i.e., uses [, instead of [[? Maybe sblapply for single bracket? I was also
> > thinking it would be nice to have an apply function for Seqinfo objects
> > that would apply over the subranges of all of the sequences, where the size
> > of the subregion is specified by the user. Maybe call it glapply, where 'g'
> > is for 'genome'?
> >
> > Michael
> >
> >    [[alternative HTML version deleted]]
> >
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