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.