Sorry, I didn't mean to indicate that I was talking just about
parallelization. The need is for a general apply function that uses [
instead [[. This usually comes up in Vectors that are not Lists, like
GRanges or Seqinfo. For GRangesList, lapply works as intended, and as
Martin says, it's usually best not to apply at all. Sometimes, however, it
is easiest to just apply. For example, if I wanted to apply over the
chromosomes, and performing some operation based on the range of the entire
chromosome, then for some Seqinfo of interest, I could do:

sblapply(si, fun) or sblapply(as(si, "GenomicRanges"), fun)

The primary use case really is something like applying over chromosomes,
which is why I suggested the high-level glapply for traversing the whole
genome.  Of course, we want this to support parallel computing, so the
region-size feature was to get around the uneven lengths of chromosomes,
which make it difficult to make effective use of resources.

Michael

On Mon, Sep 24, 2012 at 7:16 AM, Tim Triche, Jr. <tim.triche@gmail.com>wrote:

> Did you see Malcolm Cook's post recently about fixing pvec() to
> automatically do this?
>
> It seems like a sensible approach to me
>
> --t
>
> On Sep 24, 2012, at 6:53 AM, Michael Lawrence <lawrence.michael@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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>

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