NAME

Bio::DOOP::Util::Run::GeneMerge - GeneMerge based GO analyzer

VERSION

Version 0.01

SYNOPSIS

#!/usr/bin/perl -w

use Bio::DOOP::DOOP;

$test = Bio::DOOP::Util::Run::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 described in :

Cristian I. Castillo-Davis and Daniel L. Hartl 
GeneMerge—post-genomic analysis, data mining, and hypothesis testing
Bioinformatics Vol. 19 no. 7 2003, Pages 891-892

The original program is not really good for large scale analysis, 
because the design uses a lot of I/O processes. This version takes
everything into memory at start.

AUTHORS

Tibor Nagy, Godollo, Endre Sebestyen, Martonvasar,

METHODS

new

This is the constructor.

getAssocFile

The method loads the GO association file and stores it in memory.

getPopFile

The method loads the Population file and stores it in memory.

popFreq

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

getDescFile

The method loads the GO description file.

getStudyFile

The method loads the study data set.

getResults

The method gives back all the results.

hypergeometric

This 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.

cpanm Bio::DOOP::DOOP

perl -MCPAN -e shell
install Bio::DOOP::DOOP