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GO-TermFinder-0.7
River stage zero No dependents
++

Changes for version 0.70 - 2004-11-18

  • GO::TermFinder
  • Now uses an entirely new set of code for calculating the probability based on the hypergeometric distribution (written by Ihab Awad). The new code is written in C++, and interfaced to Perl using SWIG. For long running batch jobs, with > 100 lists of genes (using for instance analyze.pl in the examples directory), the new code is up to 3 times faster. Note, that installation now requires an ANSI C++ compiler - see the README for more details.
  • Note that the ability to use the binomial distribution for the probability calculation no longer exists - it will always use the hypergeometric distribution now.
  • GO::Utils::File
  • fixed small bug in that only one leading space would be stripped from a gene name in GenesFromFile - thanks to Linda McMahan at Princeton for spotting this one.
  • GO::TermFinder
  • made error message a little more explicit when a goid used to annotate a gene (as indicated by the annotation provider) does not appear in the provided ontology - thanks to John Matese for the suggestion.
  • GO::View
  • small addition that hopefully deals with a problem sometimes seen when running on Windows, that I think is due to line endings produced by the dot program.

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