/ 
Bio-DOOP-DOOP-1.00
/ Bio::DOOP::Util::Run::GeneMerge

NAME

Bio::GeneMerge - GeneMerge based GO analyzer

VERSION

Version 0.01

SYNOPSIS

#!/usr/bin/perl -w

use Bio::GeneMerge;

$test = Bio::GeneMerge->new();

if ($test->getDescFile("GO/use/GO.BP.use") < 0){
   print"Desc error\n"
}

if ($test->getAssocFile("GO/assoc/A_thaliana.converted.BP") < 0){
   print"Assoc error\n"
}

if ($test->getPopFile("GO/pop.500") < 0){
   print"Pop error\n"
}

if ($test->getStudyFile("GO/study.500/combined1314.list") < 0){
   print"Study error\n"
}

$results = $test->getResults();

foreach $res (@{$results}) {
   print $$res{'GOterm'}," ",$$res{'RawEs'},"\n";
}

DESCRIPTION

This is a module based on GeneMerge v1.2. Original program
created by Cristian I. Castillo-Davis (castill0@stat.umd.edu)

Post-genomic analysis, data mining, and hypotesis testing.
The original program is not too good for large scale analysis, 
because the design use a lot of I/O process. This version is
take the whole process into the memory.

AUTHORS

Tibor Nagy, Godollo, Endre Sebestyen, Martonvasar,
Cristian I. Castillo-Davis,

METHODS

new

This is the constructor.

getAssocFile

The method load the GO association file and store it in memory.

getPopFile

The method load the Population file and store it in memory.

popFreq

The method calculate the population frequency.
Do not use it directly.

getDescFile

The method load the GO description file.

getStudyFile

The method loads the study data set.

getResults

The method give back all the results

hypergeometric

It is an internal function to calculate the 
hypergeometric distribution. Do not use it directly.

logNchooseK

Another internal function for the correct statistical results.
Do not use it directly.

lFactorial

Factorial calculating function.
Do not use it directly.