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topGO (version 2.20.0)

topGO: 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

2.20.0

License

LGPL

Maintainer

Adrian Alexa

Last Published

February 15th, 2017

Functions in topGO (2.20.0)

elimScore-class

Classes "elimScore" and "weight01Score"

dignostic-methods

Diagnostic functions for topGOdata and topGOresult objects.

Determines the levels of a Directed Acyclic Graph (DAG)

Utility functions to work with Directed Acyclic Graphs (DAG)

annFUN

Functions which map gene identifiers to GO terms

classicCount-class

Class "classicCount"

elimCount-class

Classes "elimCount" and "weight01Count"

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

elimExpr-class

Class "elimExpr"

groupGOTerms

Grouping of GO terms into the three ontologies

printGraph-methods

Visualisation functions

inducedGraph

The subgraph induced by a set of nodes.

groupStats-class

Class "groupStats"

parentChild-class

Classes "parentChild" and "pC"

getSigGroups

Interfaces for running the enrichment tests

getPvalues

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

topGO-package

Enrichment analysis for Gene Ontology

GOdata

Sample topGOdata and topGOresult objects

Gene set tests statistics