Just a note: the foreach package has solved this by providing a
"nesting" operator, which effectively converts multiple nested foreach
loops into one big one:
http://cran.r-project.org/web/packages/foreach/vignettes/nested.pdf
On Thu 14 Nov 2013 09:24:29 AM PST, Michael Lawrence wrote:
I like the general idea of having iterators; was just checking out the
itertools package after not having looked at it for a while. I could see
having a BiocIterators package, and a bpiterate(iterator, FUN, ...,
BPPARAM). My suggestion was simpler though. Right now, bpmapply runs a
single job per iteration, which is fine; the flattening could just be made
more convenient.
On Thu, Nov 14, 2013 at 8:47 AM, Michel Lang <michell...@gmail.com> wrote:
We use a design iterator in BatchExperiments::makeDesign for a cartesian
product. I found a old version of designIterator (cf. <
https://github.com/tudo-r/BatchExperiments/blob/master/R/designs.R>) w/o
the optional data.frame input which is easier to read: <
https://gist.github.com/mllg/7469844>.
AFAIR the speed was decent. Major advantage is the low memory footprint.
Could easily be ported to a reference class and should run on arbitrary
objects with small modifications.
In parallel it might get tricky though. You could try to sequentially
request [n] elements of the iterator, chunk them to match [desired number
of jobs] and then parallelize. Or write a function which converts a single
integer to the respective integer vector "state" in above referenced gist
which is in my opinion much more flexible.
2013/11/14 Michael Lawrence <lawrence.mich...@gene.com>
Hi guys,
We often need to iterate over the cartesian product of two dimensions,
like sample X chromosome. This is preferable to nested iteration, which
is
complicated. I've been using expand.grid and bpmapply for this, but it
seems like this could be made easier. Like bpmapply could gain a
CARTESIAN
argument with a list of arguments to multiply? But somehow you would want
the resuls combined in a way that does not require generating the product
manually. Maybe a list of lists? We need to think more about the
combination step, in general.
Michael
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