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GO-TermFinder-0.81
River stage zero No dependents
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Changes for version 0.81 - 2008-05-13

  • GO::TermFinder
  • Made totalNumGenes a public method, which returns the total number of genes that are in the background set of genes from which the genes of interest were drawn. Unannotated genes are included in this count. This allowed me to fix a bug in analyze.pl, where it didn't always report the correct number of genes in the background.
  • GO::AnnotationProvider::AnnotationParser
  • Fixed bug in handling a name that was ambiguous when considered in a case-insensitive fashion, but unambiguous when considered in a case-sensitive fashion. Thanks to Robert Flight for the bug report.
  • GO::OntologyProvider::OboParser
  • Added additional logic to detect an error in the obo file if a node and a parent are in different namespaces, as this previously produced a fatal error with a cryptic message.
  • GO::TermFinder
  • Prevent crash that could occur when there were no GO nodes tested - assertion that correction factor had to be >=1 was incorrect in this case, which could cause the script to die. Now correctly recognizes this. Thanks to Mark Schroeder at Princeton for pointing this out.
  • GO::View
  • I had previously commented out a check, that resulted in postscript images always being generated. Now they are only generated when requested.
  • GO-TermFinder-Obo.t
  • Tweaked test to be regex instead of equality, as different Perls might add different things to exceptions. This fixes a failure I was seeing on Solaris.

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