# topGO: Enrichment analysis for Gene Ontology

## Documentation for package ‘topGO’ version 2.2.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

A B C D E F G I J L M N O P R S T U W

## -- --

topGO-package | Enrichment analysis for Gene Ontology

## -- A --

affyLib | A toy example of a list of gene identifiers and the respective p-values
algorithm | Class "topGOresult"
algorithm-method | Class "topGOresult"
algorithm<- | Class "topGOresult"
algorithm<--method | Class "topGOresult"
allGenes | Class "topGOdata"
allGenes-method | Class "topGOdata"
allMembers | Class "groupStats"
allMembers-method | Class "elimExpr"
allMembers-method | Classes "elimScore" and "weight01Score"
allMembers-method | Class "groupStats"
allMembers-method | Classes "parentChild" and "pC"
allMembers-method | Class "weightCount"
allMembers<- | Class "groupStats"
allMembers<--method | Class "classicExpr"
allMembers<--method | Class "groupStats"
allMembers<--method | Classes "parentChild" and "pC"
allParents | Classes "parentChild" and "pC"
allParents-method | Classes "parentChild" and "pC"
allScore | Class "classicScore"
allScore-method | Class "classicScore"
allScore-method | Classes "elimScore" and "weight01Score"
alternative-method | Classes "elimScore" and "weight01Score"
annFUN | Functions which map gene identifiers to GO terms
annFUN.db | Functions which map gene identifiers to GO terms
annFUN.file | Functions which map gene identifiers to GO terms
annFUN.gene2GO | Functions which map gene identifiers to GO terms
annFUN.GO2genes | Functions which map gene identifiers to GO terms
annFUN.org | Functions which map gene identifiers to GO terms
attrInTerm | Class "topGOdata"
attrInTerm-method | Class "topGOdata"

## -- B --

buildLevels | Utility functions to work with Directed Acyclic Graphs (DAG)

## -- C --

classicCount-class | Class "classicCount"
classicExpr-class | Class "classicExpr"
classicScore-class | Class "classicScore"
combineResults | Class "topGOresult"
contTable | Class "classicCount"
contTable-method | Class "classicCount"
contTable-method | Classes "elimCount" and "weight01Count"
countGenesInTerm | Class "topGOdata"
countGenesInTerm-method | Class "topGOdata"
cutOff | Classes "elimCount" and "weight01Count"
cutOff-method | Classes "elimCount" and "weight01Count"
cutOff-method | Class "elimExpr"
cutOff-method | Classes "elimScore" and "weight01Score"
cutOff<- | Classes "elimCount" and "weight01Count"
cutOff<--method | Classes "elimCount" and "weight01Count"
cutOff<--method | Class "elimExpr"
cutOff<--method | Classes "elimScore" and "weight01Score"

## -- D --

depth | Classes "elimCount" and "weight01Count"
depth-method | Classes "elimCount" and "weight01Count"
depth-method | Class "elimExpr"
depth-method | Classes "elimScore" and "weight01Score"
depth<- | Classes "elimCount" and "weight01Count"
depth<--method | Classes "elimCount" and "weight01Count"
depth<--method | Class "elimExpr"
depth<--method | Classes "elimScore" and "weight01Score"
description | Class "topGOdata"
description-method | Class "topGOdata"
description-method | Class "topGOresult"
description<- | Class "topGOdata"
description<--method | Class "topGOdata"
description<--method | Class "topGOresult"

## -- E --

elim | Classes "elimCount" and "weight01Count"
elim-method | Classes "elimCount" and "weight01Count"
elim-method | Class "elimExpr"
elim-method | Classes "elimScore" and "weight01Score"
elim<- | Classes "elimCount" and "weight01Count"
elim<--method | Classes "elimCount" and "weight01Count"
elim<--method | Class "elimExpr"
elim<--method | Classes "elimScore" and "weight01Score"
elimCount-class | Classes "elimCount" and "weight01Count"
elimExpr-class | Class "elimExpr"
elimScore-class | Classes "elimScore" and "weight01Score"
emptyExpr-method | Class "classicExpr"
expressionMatrix | Class "topGOdata"
expressionMatrix-method | Class "topGOdata"

## -- F --

feasible | Class "topGOdata"
feasible-method | Class "topGOdata"
feasible<- | Class "topGOdata"
feasible<--method | Class "topGOdata"

## -- G --

geneData | Class "topGOresult"
geneData-method | Class "topGOresult"
geneData<- | Class "topGOresult"
geneData<--method | Class "topGOresult"
geneList | A toy example of a list of gene identifiers and the respective p-values
genes | Class "topGOdata"
genes-method | Class "topGOdata"
geneScore | Class "topGOdata"
geneScore-method | Class "topGOdata"
geneSelectionFun | Class "topGOdata"
geneSelectionFun-method | Class "topGOdata"
geneSelectionFun<- | Class "topGOdata"
geneSelectionFun<--method | Class "topGOdata"
genesInTerm | Class "topGOdata"
genesInTerm-method | Class "topGOdata"
GenTable | Diagnostic functions for topGOdata and topGOresult objects.
GenTable-method | Diagnostic functions for topGOdata and topGOresult objects.
getGraphRoot | Utility functions to work with Directed Acyclic Graphs (DAG)
getNoOfLevels | Utility functions to work with Directed Acyclic Graphs (DAG)
getPvalues | Convenient function to compute p-values from a gene expression matrix.
getSigGroups | Interfaces for running the enrichment tests
getSigGroups-method | Interfaces for running the enrichment tests
getSigGroups-methods | Interfaces for running the enrichment tests
getSigRatio | Class "weightCount"
getSigRatio-method | Class "weightCount"
GOBPTerm | Grouping of GO terms into the three ontologies
GOCCTerm | Grouping of GO terms into the three ontologies
GOdata | Sample topGOdata and topGOresult objects
GOFisherTest | Gene set tests statistics
GOFisherTest-method | Class "classicCount"
GOFisherTest-method | Classes "elimCount" and "weight01Count"
GOglobalTest | Gene set tests statistics
GOglobalTest-method | Class "classicExpr"
GOKSTest | Gene set tests statistics
GOKSTest-method | Class "classicScore"
GOKSTiesTest | Gene set tests statistics
GOKSTiesTest-method | Class "classicScore"
GOMFTerm | Grouping of GO terms into the three ontologies
GOplot | Visualisation functions
GOSumTest | Gene set tests statistics
GOSumTest-method | Class "classicScore"
GOtTest | Gene set tests statistics
GOtTest-method | Class "classicScore"
graph | Class "topGOdata"
graph-method | Class "topGOdata"
graph<- | Class "topGOdata"
graph<--method | Class "topGOdata"
groupGOTerms | Grouping of GO terms into the three ontologies
groupStats-class | Class "groupStats"

## -- I --

inducedGraph | The subgraph induced by a set of nodes.
initialize-method | Class "classicCount"
initialize-method | Class "classicExpr"
initialize-method | Class "classicScore"
initialize-method | Classes "elimCount" and "weight01Count"
initialize-method | Class "elimExpr"
initialize-method | Classes "elimScore" and "weight01Score"
initialize-method | Class "groupStats"
initialize-method | Classes "parentChild" and "pC"
initialize-method | Class "topGOdata"
initialize-method | Class "topGOresult"
initialize-method | Class "weightCount"
inverseList | Functions which map gene identifiers to GO terms

## -- J --

joinFun | Classes "parentChild" and "pC"
joinFun-method | Classes "parentChild" and "pC"

## -- L --

leaCount-class | Classes "elimCount" and "weight01Count"
leaExpr-class | Class "elimExpr"
leaScore-class | Classes "elimScore" and "weight01Score"

## -- M --

members | Class "groupStats"
members-method | Class "elimExpr"
members-method | Classes "elimScore" and "weight01Score"
members-method | Class "groupStats"
members-method | Class "weightCount"
members<- | Class "groupStats"
members<--method | Class "groupStats"
membersExpr | Class "classicExpr"
membersExpr-method | Class "classicExpr"
membersScore | Class "classicScore"
membersScore-method | Class "classicScore"
membersScore-method | Classes "elimScore" and "weight01Score"

## -- N --

Name | Class "groupStats"
Name-method | Class "groupStats"
Name-method | Class "weightCount"
Name<- | Class "groupStats"
Name<--method | Class "groupStats"
nodesInInducedGraph | The subgraph induced by a set of nodes.
numAllMembers | Class "groupStats"
numAllMembers-method | Classes "elimCount" and "weight01Count"
numAllMembers-method | Class "elimExpr"
numAllMembers-method | Classes "elimScore" and "weight01Score"
numAllMembers-method | Class "groupStats"
numAllMembers-method | Classes "parentChild" and "pC"
numAllMembers-method | Class "weightCount"
numGenes | Class "topGOdata"
numGenes-method | Class "topGOdata"
numMembers | Class "groupStats"
numMembers-method | Classes "elimCount" and "weight01Count"
numMembers-method | Class "elimExpr"
numMembers-method | Classes "elimScore" and "weight01Score"
numMembers-method | Class "groupStats"
numMembers-method | Class "weightCount"
numSigAll | Class "classicCount"
numSigAll-method | Class "classicCount"
numSigAll-method | Classes "elimCount" and "weight01Count"
numSigAll-method | Classes "parentChild" and "pC"
numSigAll-method | Class "weightCount"
numSigGenes | Class "topGOdata"
numSigGenes-method | Class "topGOdata"
numSigMembers | Class "classicCount"
numSigMembers-method | Class "classicCount"
numSigMembers-method | Classes "elimCount" and "weight01Count"
numSigMembers-method | Class "weightCount"

## -- O --

ontology | Class "topGOdata"
ontology-method | Class "topGOdata"
ontology<- | Class "topGOdata"
ontology<--method | Class "topGOdata"

## -- P --

parentChild-class | Classes "parentChild" and "pC"
pC-class | Classes "parentChild" and "pC"
penalise | Class "weightCount"
penalise-method | Class "weightCount"
permSumStats | Gene set tests statistics
permSumStats.all | Gene set tests statistics
phenotype | Class "topGOdata"
phenotype-method | Class "topGOdata"
print-method | Class "topGOdata"
print-method | Class "topGOresult"
printGenes | Diagnostic functions for topGOdata and topGOresult objects.
printGenes-method | Diagnostic functions for topGOdata and topGOresult objects.
printGenes-methods | Diagnostic functions for topGOdata and topGOresult objects.
printGraph | Visualisation functions
printGraph-method | Visualisation functions
printGraph-methods | Visualisation functions
pType | Class "classicExpr"
pType-method | Class "classicExpr"
pType<- | Class "classicExpr"
pType<--method | Class "classicExpr"

## -- R --

rankMembers | Class "classicScore"
rankMembers-method | Class "classicScore"
rankMembers-method | Classes "elimScore" and "weight01Score"
readMappings | Functions which map gene identifiers to GO terms
resultFisher | Sample topGOdata and topGOresult objects
resultKS | Sample topGOdata and topGOresult objects
reverseArch | Utility functions to work with Directed Acyclic Graphs (DAG)
roundFun | Class "weightCount"
roundFun-method | Class "weightCount"
runTest | Interfaces for running the enrichment tests
runTest-method | Interfaces for running the enrichment tests
runTest-method | Class "groupStats"

## -- S --

score | Class "topGOresult"
score-method | Class "topGOresult"
score<- | Class "classicScore"
score<--method | Class "classicScore"
score<--method | Classes "elimScore" and "weight01Score"
score<--method | Class "topGOresult"
scoreOrder | Class "classicScore"
scoreOrder-method | Class "classicScore"
scoresInTerm | Class "topGOdata"
scoresInTerm-method | Class "topGOdata"
show-method | Class "topGOdata"
show-method | Class "topGOresult"
showGroupDensity | Diagnostic functions for topGOdata and topGOresult objects.
showSigOfNodes | Visualisation functions
sigAllMembers | Class "classicCount"
sigAllMembers-method | Class "classicCount"
sigAllMembers-method | Classes "elimCount" and "weight01Count"
sigAllMembers-method | Classes "parentChild" and "pC"
sigGenes | Class "topGOdata"
sigGenes-method | Class "topGOdata"
sigMembers | Class "classicCount"
sigMembers-method | Class "classicCount"
sigMembers-method | Classes "elimCount" and "weight01Count"
sigMembers<- | Class "classicCount"
sigMembers<--method | Class "classicCount"
sigMembers<--method | Classes "elimCount" and "weight01Count"
sigMembers<--method | Classes "parentChild" and "pC"
significant | Class "weightCount"
significant-method | Class "weightCount"
sigRatio | Class "weightCount"
sigRatio-method | Class "weightCount"
sigRatio<- | Class "weightCount"
sigRatio<--method | Class "weightCount"

## -- T --

termStat | Class "topGOdata"
termStat-method | Class "topGOdata"
testName | Class "topGOresult"
testName-method | Class "topGOresult"
testName<- | Class "topGOresult"
testName<--method | Class "topGOresult"
testStatistic | Class "groupStats"
testStatistic-method | Class "groupStats"
testStatistic-method | Class "weightCount"
testStatPar | Class "groupStats"
testStatPar-method | Class "groupStats"
testStatPar-method | Class "weightCount"
topDiffGenes | A toy example of a list of gene identifiers and the respective p-values
topGO | Enrichment analysis for Gene Ontology
topGOdata-class | Class "topGOdata"
topGOresult-class | Class "topGOresult"

## -- U --

updateGenes | Class "topGOdata"
updateGenes-method | Class "topGOdata"
updateGroup | Class "groupStats"
updateGroup-method | Class "groupStats"
updateGroup-method | Classes "parentChild" and "pC"
updateGroup-method | Class "weightCount"
updateTerm<- | Class "topGOdata"
updateTerm<--method | Class "topGOdata"
usedGO | Class "topGOdata"
usedGO-method | Class "topGOdata"

## -- W --

weight01Count-class | Classes "elimCount" and "weight01Count"
weight01Expr-class | Class "elimExpr"
weight01Score-class | Classes "elimScore" and "weight01Score"
weightCount-class | Class "weightCount"
Weights | Class "weightCount"
Weights-method | Class "weightCount"
Weights<- | Class "weightCount"
Weights<--method | Class "weightCount"
whichAlgorithms | Interfaces for running the enrichment tests
whichTests | Interfaces for running the enrichment tests