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GO-TermFinder-0.72
River stage zero No dependents

Changes for version 0.72 - 2006-07-27

  • GO::TermFinder
  • Forgot to have the __saveVariables method save the discarded genes when simulations were being run, or the FDR was being calculated. Consequently, this information was being lost if either FDR or simulations were requested. This is now fixed.
  • Found a minor buglet, concerning how genes were selected for simulations if a population had been used. This didn't affect the actual results, but now is *slightly* faster.
  • General
  • Started using the Test::Spelling module locally, and it found a few typos that have been corrected.

Modules

GO::AnnotatedGene
GO::Annotation
GO::AnnotationProvider
abstract base class defining interface for how Annotation information should be provided
GO::AnnotationProvider::AnnotationParser
parses a gene annotation file
GO::Node
provides information about a node in the Gene Ontology
GO::OntologyProvider
abstract base class providing API for the provision on Gene Ontology information
GO::OntologyProvider::OntologyParser
Provides API for retrieving data from Gene Ontology files
GO::Reference
GO::TermFinder
identify GO nodes that annotate a group of genes with a significant p-value
GO::TermFinderReport::Html
prints an html table of the results of GO::TermFinder
GO::TermFinderReport::Text
prints results of GO::TermFinder as a text report
GO::Utils::File
simply utility module for dealing with file parsing
GO::Utils::General
provides some general utilities for clients of other GO classes
GO::View
Creates a gif or png image for visualizing the GO DAG
GO::View::GD
a helper class for GO::View to deal with the image

Provides

GO::TermFinder::Native
in lib/GO/TermFinder/Native.pm
GO::TermFinder::Native::Distributions
in lib/GO/TermFinder/Native.pm
GO::TermFinder::Nativec
in lib/GO/TermFinder/Native.pm

Examples

Other files