Bio::DOOP::Util::Run::GeneMerge - GeneMerge based GO analyzer
Version 0.01
#!/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"; }
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.
Tibor Nagy, Godollo, Endre Sebestyen, Martonvasar,
This is the constructor.
The method loads the GO association file and stores it in memory.
The method loads the Population file and stores it in memory.
The method calculates the population frequency. Do not use it directly.
The method loads the GO description file.
The method loads the study data set.
The method gives back all the results.
This is an internal function to calculate the hypergeometric distribution. Do not use it directly.
Another internal function for the correct statistical results. Do not use it directly.
Factorial calculating function. Do not use it directly.
1 POD Error
The following errors were encountered while parsing the POD:
Non-ASCII character seen before =encoding in 'GeneMerge—post-genomic'. Assuming UTF-8
To install Bio::DOOP::DOOP, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::DOOP::DOOP
CPAN shell
perl -MCPAN -e shell install Bio::DOOP::DOOP
For more information on module installation, please visit the detailed CPAN module installation guide.