[Buffalo-pm] Statistics With Perl...

DANIEL MAGNUSZEWSKI dmagnuszewski at mandtbank.com
Wed Jan 18 20:17:59 PST 2006


Ganesh,

Correct me if I'm wrong, but you mentioned last night that
Bioinformatics is beginning to focus more on the statistics and
probability of test results being correct and less on the actual lower
level programming aspects (such as using Perl to do sequencing and give
you the test results, etc). This is because of the large code base that
is already in place. You then mentioned that because of this, people
within Bioinformatics (in general) will begin to move away from Perl,
and begin to use a language like R (http://www.r-project.org/). After we
mentioned how there was probably a wrapper module for R, I poked around
CPAN and found a module, Statistics::R, that will allow you to interact
(create, start, stop, etc) with an R interpreter through Perl.

Statistics::R - Controls the R (R-project) interpreter through Perl.

http://search.cpan.org/~gmpassos/Statistics-R-0.02/lib/Statistics/R.pm

Below is another R module I found, but it states that it doesn't
implement all functions of R - so I'm assuming that it can be quite
limiting:

PDL::R::math - routines from statistics language, R, for PDL

http://search.cpan.org/~cavanaugh/PDL-R-math-0.12/rmath.pd

Also, I'm not sure if you use programs like MATLAB, but there is an open
source version of it called Octave (http://www.octave.org). As with most
everything, there are some Perl modules available to help you interact
with it:

Inline::Octave - Inline octave code into your Perl

http://search.cpan.org/~aadler/Inline-Octave-0.22/Octave.pm

I have even found a package available that will provide an interface
between R and Octave - properly named, ROctave (
http://www.omegahat.org/ROctave/ ). The same group that releases
ROctave, has a package called RSPerl ( http://www.omegahat.org/RSPerl/ )
that "provides a bidirectional interface for calling R from Perl and
Perl from R". Essentially, these tools provide statistical functionality
to Perl that is not natively present.

Does any of this seem useful for what Biologist need to do? Would this
integrated "framework" help for creating better/more effective tools? 

Hopefully some of this helps...

-Dan




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