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GO-TermFinder-0.83
River stage zero No dependents
++

Changes for version 0.83 - 2009-01-22

  • Changed the way in which genes are rendomly chosen from the background distribution, when calculating FDR, due to a bias that existed in the algorithm. Thanks to Peter Wentzell for pointing this out; also see:
  • Flight, R.M and Wentzell, P.D. (2009). Potential Bias in GO::TermFinder. Briefings in Bioinformatics, in press.
  • In my testing, this improves the FDR when having passed in a list of genes as a background population from which the test set were drawn. For some reason, it seems to make less significant (higher FDR) those values calculated when the background population of genes is not passed in (and is assumed to be all genes).

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::OboParser
Provides API for retrieving data from Gene Ontology obo file.
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