topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.
|Author||Adrian Alexa, Jorg Rahnenfuhrer|
|Date of publication||None|
|Maintainer||Adrian Alexa <email@example.com>|
annFUN: Functions which map gene identifiers to GO terms
classicCount-class: Class "classicCount"
classicExpr-class: Class "classicExpr"
classicScore-class: Class "classicScore"
dagFunctions: Utility functions to work with Directed Acyclic Graphs (DAG)
diagnosticMethods: Diagnostic functions for topGOdata and topGOresult objects.
elimCount-class: Classes "elimCount" and "weight01Count"
elimExpr-class: Class "elimExpr"
elimScore-class: Classes "elimScore" and "weight01Score"
geneList: A toy example of a list of gene identifiers and the...
getPvalues: Convenient function to compute p-values from a gene...
getSigGroups: Interfaces for running the enrichment tests
GOdata: Sample topGOdata and topGOresult objects
GOTests: Gene set tests statistics
groupGOTerms: Grouping of GO terms into the three ontologies
groupStats-class: Class "groupStats"
inducedGraph: The subgraph induced by a set of nodes.
parentChild-class: Classes "parentChild" and "pC"
printGraph-methods: Visualisation functions
topGOdata-class: Class "topGOdata"
topGO-package: Enrichment analysis for Gene Ontology
topGOresult-class: Class "topGOresult"
weightCount-class: Class "weightCount"