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.
1 POD Error
The following errors were encountered while parsing the POD:
- Around line 56:
Non-ASCII character seen before =encoding in 'GeneMerge—post-genomic'. Assuming UTF-8