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GO-TermFinder-0.8
River stage zero No dependents

Changes for version 0.80 - 2007-03-22

  • GO::OntologyProvider::OboParser
  • New module, contributed by Shuai Weng of SGD. This allows you to use the .obo files instead of the .ontology files. The .ontology files have been deprecated for a while, and are much bigger than the .obo version, as they contain redundant information. The ontology parsing module still ships, but will be deprecated in future versions. The test suite for the ontology parser no longer ships with the distribution, though I still test it locally.
  • Note, the API for the OboParser is slightly different, in that you have to provide the aspect of the ontology that you want (P, C or F), which was not the case when parsing the .ontology files.
  • All the example code in the examples/ directory has been updated to work with the obo parser.
  • GO::TermFinder
  • Updated to deal with the loss of the 'unknown' nodes in the ontology. With the removal of those nodes, direct annotation to the aspect node, such as biological_process, is meaningful. Thus, it now tests for significance for genes annotated directly to the aspect nodes, ignoring indirect annotations to those nodes.
  • Added an additional check, such that if you provide a background population, but none of the genes in your list of interest are in that population, it dies with a useful error message (as opposed to the previously useless one).
  • Corrected a bug in the Bonferroni correction, where it was too conservative - not sure what I was thinking.
  • GO::TermFinderReport::Text
  • Can now print out the results in tabular form, instead of the usual text version, to help with automated analyses. Thanks to Noah Zimmerman for the code changes.
  • Code Quality
  • I have started to use Perl::Critic locally, and all the code at least passes level 5. Future revisions will pass harsher review (with some rules commented out!).
  • Compilation
  • The native/Makefile.PL has been modified to hopefully make it compile correctly under Cygwin - thanks to Noah Zimmerman for help with testing.

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