[BioC] R + SNOW scripts

Steve Lianoglou mailinglist.honeypot at gmail.com
Tue Oct 23 00:30:01 CEST 2012


On Mon, Oct 22, 2012 at 6:08 PM, Blesson Varghese
<blssnvarghese at gmail.com> wrote:
> Hi
> I am a very new user to the Bioconductor packages. I was wondering if
> there are any sample codes within the bioconductor package that uses
> R+ SNOW combination or pointers to any sample code?

You'd get a lot better help if you perhaps provided some specific
examples of what you want to accomplish, and what you have tried.

The latter part of my last sentence implies that you have already done
some homework about parallel computation with R -- there are many
places to look, such as the "foreach" family of packages (along with
doParallel, doMPI, doSNOW), the "parallel" package, etc.

There is really nothing all that special about applying these packages
to "bioconductor" code, so ... feel free to go ahead and start

That having been said, you can download the source code for the
ShortRead package and try to wrap your mind around the code in the
R/srapply.R file if you were *literally* looking for parallelized code
actually "in bioconductor". The `srapply` function somehow generalizes
over running code in parallel on both a multicore machine (via the
`parallel` package) as well as over a cluster (using `Rmpi`) --
neither of those use the `snow` package, but my guess is that you
don't really want to know *only* about the snow package.


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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