topGO (version 2.24.0)

Enrichment Analysis for Gene Ontology

Description

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.

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Version

2.24.0

License

LGPL

Maintainer

Adrian Alexa

Last Published

February 15th, 2017

Functions in topGO (2.24.0)

Gene set tests statistics

classicCount-class

Class "classicCount"

inducedGraph

The subgraph induced by a set of nodes.

groupGOTerms

Grouping of GO terms into the three ontologies

getSigGroups

Interfaces for running the enrichment tests

classicExpr-class

Class "classicExpr"

Determines the levels of a Directed Acyclic Graph (DAG)

Utility functions to work with Directed Acyclic Graphs (DAG)

topGOdata-class

Class "topGOdata"

geneList

A toy example of a list of gene identifiers and the respective p-values

elimScore-class

Classes "elimScore" and "weight01Score"

classicScore-class

Class "classicScore"

printGraph-methods

Visualisation functions

topGO-package

Enrichment analysis for Gene Ontology

GOdata

Sample topGOdata and topGOresult objects

dignostic-methods

Diagnostic functions for topGOdata and topGOresult objects.

groupStats-class

Class "groupStats"

elimCount-class

Classes "elimCount" and "weight01Count"

parentChild-class

Classes "parentChild" and "pC"

topGOresult-class

Class "topGOresult"

getPvalues

Convenient function to compute p-values from a gene expression matrix.

elimExpr-class

Class "elimExpr"

annFUN

Functions which map gene identifiers to GO terms

weightCount-class

Class "weightCount"