Tibor Nagy > Bio-DOOP-DOOP-1.02 > Bio::DOOP::Util::Run::GeneMerge

Download:
Bio-DOOP-DOOP-1.02.tar.gz

Dependencies

Annotate this POD

View/Report Bugs
Module Version: 0.01   Source   Latest Release: Bio-DOOP-DOOP-1.04

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.
syntax highlighting: