Changes for version 0.60 - 2004-05-05
- GO::TermFinder
- The multiple hypothesis correction is no longer done using the custom method, but instead uses a Bonferroni correction.
- Correcting p-values by running simulations is now available, to allow you to control the Family Wise Error rate.
- Added the ability to calculate the False Discovery Rate, as a potential means of avoiding the whole p-value problem.
- see the pod for GO::TermFinder, as well as docs/GO-TermFinder.doc for more information on these.
- tools
- updated the batchGOView.pl tool, and the analyze.pl tool, in the examples directory, to support printing out of the False Discovery Rate if calculated. They also both use the newly created GO::TermFinderReport::Text object, to consolidate code, and to keep their reports consistent with one another.
- README
- Tried to make it a little clearer as to how to install the libraries.
Modules
abstract base class defining interface for how Annotation information should be provided
parses a gene annotation file
provides information about a node in the Gene Ontology
abstract base class providing API for the provision on Gene Ontology information
Provides API for retrieving data from Gene Ontology files
identify GO nodes that annotate a group of genes with a significant p-value
prints an html table of the results of GO::TermFinder
prints results of GO::TermFinder as a text report
simply utility module for dealing with file parsing
provides some general utilities for clients of other GO classes
Creates a gif or png image for visualing the GO DAG
a helper class for GO::View to deal with the image
