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.

cpanm Bio::DOOP::DOOP

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