# topGO: Enrichment analysis for Gene Ontology

## Documentation for package ‘topGO’ version 1.8.1

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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

## -- --

topGO-package | Enrichment analysis for Gene Ontology

## -- A --

allGenes | Class "topGOdata"
allGenes,topGOdata-method | Class "topGOdata"
allMembers | Class "groupStats"
allMembers,elimScore-method | Classes "elimScore" and "removeScore"
allMembers,groupStats-method | Class "groupStats"
allMembers,parentChild-method | Classes "parentChild" and "pC"
allMembers,removeExpr-method | Class "elimExpr" ~~~
allMembers,removeScore-method | Classes "elimScore" and "removeScore"
allMembers,weightCount-method | Class "weightCount"
allMembers<-,classicExpr-method | Class "classicExpr" ~~~
allMembers<-,groupStats-method | Class "groupStats"
allMembers<-,parentChild-method | Classes "parentChild" and "pC"
allMembers<-,pC-method | Classes "parentChild" and "pC"
allParents | Classes "parentChild" and "pC"
allParents,parentChild-method | Classes "parentChild" and "pC"
allScore | Class "classicScore"
allScore,classicScore,logical-method | Class "classicScore"
allScore,classicScore,missing-method | Class "classicScore"
allScore,elimScore,logical-method | Classes "elimScore" and "removeScore"
allScore,elimScore,missing-method | Classes "elimScore" and "removeScore"
allScore,removeScore,logical-method | Classes "elimScore" and "removeScore"
allScore,removeScore,missing-method | Classes "elimScore" and "removeScore"
alternative,elimScore-method | Classes "elimScore" and "removeScore"
annFUN | functions to map gene IDs to GO terms
attrInTerm | Class "topGOdata"
attrInTerm,topGOdata,character,character-method | Class "topGOdata"
attrInTerm,topGOdata,character,missing-method | Class "topGOdata"

## -- B --

buildGOgraph.topology | buils GO graph starting from the most specific GO terms
buildLevels | Determines the levels of a Directed Acyclic Graph (DAG)

## -- C --

classicCount-class | Class "classicCount"
classicExpr-class | Class "classicExpr" ~~~
classicScore-class | Class "classicScore"
contTable | Class "classicCount"
contTable,classicCount-method | Class "classicCount"
contTable,elimCount-method | Classes "elimCount" and "removeCount"
countGenesInTerm | Class "topGOdata"
countGenesInTerm,topGOdata,character-method | Class "topGOdata"
countGenesInTerm,topGOdata,missing-method | Class "topGOdata"
cutOff | Classes "elimCount" and "removeCount"
cutOff,elimCount-method | Classes "elimCount" and "removeCount"
cutOff,elimExpr-method | Class "elimExpr" ~~~
cutOff,elimScore-method | Classes "elimScore" and "removeScore"
cutOff<-,elimCount-method | Classes "elimCount" and "removeCount"
cutOff<-,elimExpr-method | Class "elimExpr" ~~~
cutOff<-,elimScore-method | Classes "elimScore" and "removeScore"

## -- D --

description | Class "topGOdata"
description,topGOdata-method | Class "topGOdata"
description,topGOresult-method | Class "topGOresult"
description<-,topGOdata,ANY-method | Class "topGOdata"
description<-,topGOresult,ANY-method | Class "topGOresult"

## -- E --

elim | Classes "elimCount" and "removeCount"
elim,elimCount-method | Classes "elimCount" and "removeCount"
elim,elimScore-method | Classes "elimScore" and "removeScore"
elim,removeCount-method | Classes "elimCount" and "removeCount"
elim,removeExpr-method | Class "elimExpr" ~~~
elim,removeScore-method | Classes "elimScore" and "removeScore"
elim<-,elimCount-method | Classes "elimCount" and "removeCount"
elim<-,elimScore-method | Classes "elimScore" and "removeScore"
elim<-,removeCount-method | Classes "elimCount" and "removeCount"
elim<-,removeExpr-method | Class "elimExpr" ~~~
elim<-,removeScore-method | Classes "elimScore" and "removeScore"
elimCount-class | Classes "elimCount" and "removeCount"
elimExpr-class | Class "elimExpr" ~~~
elimScore-class | Classes "elimScore" and "removeScore"
emptyExpr,classicExpr-method | Class "classicExpr" ~~~
expressionMatrix | Class "topGOdata"
expressionMatrix,topGOdata-method | Class "topGOdata"

## -- F --

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

## -- G --

genes | Class "topGOdata"
genes,topGOdata-method | Class "topGOdata"
geneScore | Class "topGOdata"
geneScore,topGOdata,character-method | Class "topGOdata"
geneScore,topGOdata,missing-method | Class "topGOdata"
geneScore,topGOdata-method | Class "topGOdata"
geneSelectionFun | Class "topGOdata"
geneSelectionFun,topGOdata-method | Class "topGOdata"
geneSelectionFun<-,topGOdata-method | Class "topGOdata"
genesInTerm | Class "topGOdata"
genesInTerm,topGOdata,character-method | Class "topGOdata"
genesInTerm,topGOdata,missing-method | Class "topGOdata"
GenTable | Class "topGOdata"
genTable | Class "topGOdata"
genTable,topGOdata,list-method | Class "topGOdata"
GenTable,topGOdata-method | Class "topGOdata"
getGraphRoot | Determines the levels of a Directed Acyclic Graph (DAG)
getNoOfLevels | Determines the levels of a Directed Acyclic Graph (DAG)
getPvalues | Function to compute p-values of a t-test for a gene expression matrix.
getSigGroups | Algorithms for scoring GO terms
getSigGroups,topGOdata,classicCount-method | Algorithms for scoring GO terms
getSigGroups,topGOdata,classicExpr-method | Algorithms for scoring GO terms
getSigGroups,topGOdata,classicScore-method | Algorithms for scoring GO terms
getSigGroups,topGOdata,elimCount-method | Algorithms for scoring GO terms
getSigGroups,topGOdata,elimExpr-method | Algorithms for scoring GO terms
getSigGroups,topGOdata,elimScore-method | Algorithms for scoring GO terms
getSigGroups,topGOdata,parentChild-method | Algorithms for scoring GO terms
getSigGroups,topGOdata,pC-method | Algorithms for scoring GO terms
getSigGroups,topGOdata,removeCount-method | Algorithms for scoring GO terms
getSigGroups,topGOdata,removeExpr-method | Algorithms for scoring GO terms
getSigGroups,topGOdata,removeScore-method | Algorithms for scoring GO terms
getSigGroups,topGOdata,weightCount-method | Algorithms for scoring GO terms
getSigGroups-methods | Algorithms for scoring GO terms
getSigRatio | Class "weightCount"
getSigRatio,weightCount-method | Class "weightCount"
GOBPTerm | ~~function to do ... ~~
GOCCTerm | ~~function to do ... ~~
GOdata | Example of a topGO data object
GOFisherTest | Fischer's exact test for gene set
GOFisherTest,classicCount-method | Class "classicCount"
GOFisherTest,elimCount-method | Classes "elimCount" and "removeCount"
GOglobalTest | Globaltest for gene sets
GOglobalTest,classicExpr-method | Class "classicExpr" ~~~
GOKSTest | Kolmogorov-Smirnov test for gene sets
GOKSTest,classicScore-method | Class "classicScore"
GOKSTest,elimScore-method | Classes "elimScore" and "removeScore"
GOMFTerm | ~~function to do ... ~~
GOplot | ~~ Methods for Function printGraph in Package ‘topGO’ ~~
GOtTest | Kolmogorov-Smirnov test for gene sets
GOtTest,classicScore-method | Class "classicScore"
graph | Class "topGOdata"
graph,topGOdata-method | Class "topGOdata"
graph<-,topGOdata-method | Class "topGOdata"
groupGOTerms | ~~function to do ... ~~
groupStats-class | Class "groupStats"

## -- I --

inducedGraph | ~~function to do ... ~~
initialize,classicCount-method | Class "classicCount"
initialize,classicExpr-method | Class "classicExpr" ~~~
initialize,classicScore-method | Class "classicScore"
initialize,elimCount-method | Classes "elimCount" and "removeCount"
initialize,elimExpr-method | Class "elimExpr" ~~~
initialize,elimScore-method | Classes "elimScore" and "removeScore"
initialize,groupStats-method | Class "groupStats"
initialize,parentChild-method | Classes "parentChild" and "pC"
initialize,pC-method | Classes "parentChild" and "pC"
initialize,removeCount-method | Classes "elimCount" and "removeCount"
initialize,removeExpr-method | Class "elimExpr" ~~~
initialize,removeScore-method | Classes "elimScore" and "removeScore"
initialize,topGOdata-method | Class "topGOdata"
initialize,topGOresult-method | Class "topGOresult"
initialize,weightCount-method | Class "weightCount"

## -- J --

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

## -- M --

mapGenes2GOgraph | ~~function to do ... ~~
members | Class "groupStats"
members,elimScore-method | Classes "elimScore" and "removeScore"
members,groupStats-method | Class "groupStats"
members,removeExpr-method | Class "elimExpr" ~~~
members,removeScore-method | Classes "elimScore" and "removeScore"
members,weightCount-method | Class "weightCount"
members<-,groupStats-method | Class "groupStats"
membersExpr | Class "classicExpr" ~~~
membersExpr,classicExpr-method | Class "classicExpr" ~~~
membersScore | Class "classicScore"
membersScore,classicScore-method | Class "classicScore"
membersScore,elimScore-method | Classes "elimScore" and "removeScore"
membersScore,removeScore-method | Classes "elimScore" and "removeScore"

## -- N --

Name | Class "groupStats"
Name,groupStats-method | Class "groupStats"
Name,weightCount-method | Class "weightCount"
Name<-,groupStats-method | Class "groupStats"
numAllMembers | Class "groupStats"
numAllMembers,elimCount-method | Classes "elimCount" and "removeCount"
numAllMembers,elimScore-method | Classes "elimScore" and "removeScore"
numAllMembers,groupStats-method | Class "groupStats"
numAllMembers,parentChild-method | Classes "parentChild" and "pC"
numAllMembers,removeCount-method | Classes "elimCount" and "removeCount"
numAllMembers,removeExpr-method | Class "elimExpr" ~~~
numAllMembers,removeScore-method | Classes "elimScore" and "removeScore"
numAllMembers,weightCount-method | Class "weightCount"
numGenes | Class "topGOdata"
numGenes,topGOdata-method | Class "topGOdata"
numMembers | Class "groupStats"
numMembers,elimCount-method | Classes "elimCount" and "removeCount"
numMembers,elimScore-method | Classes "elimScore" and "removeScore"
numMembers,groupStats-method | Class "groupStats"
numMembers,removeCount-method | Classes "elimCount" and "removeCount"
numMembers,removeExpr-method | Class "elimExpr" ~~~
numMembers,removeScore-method | Classes "elimScore" and "removeScore"
numMembers,weightCount-method | Class "weightCount"
numSigAll | Class "classicCount"
numSigAll,classicCount-method | Class "classicCount"
numSigAll,elimCount-method | Classes "elimCount" and "removeCount"
numSigAll,parentChild-method | Classes "parentChild" and "pC"
numSigAll,removeCount-method | Classes "elimCount" and "removeCount"
numSigAll,weightCount-method | Class "weightCount"
numSigGenes | Class "topGOdata"
numSigGenes,topGOdata-method | Class "topGOdata"
numSigMembers | Class "classicCount"
numSigMembers,classicCount-method | Class "classicCount"
numSigMembers,elimCount-method | Classes "elimCount" and "removeCount"
numSigMembers,removeCount-method | Classes "elimCount" and "removeCount"
numSigMembers,weightCount-method | Class "weightCount"

## -- O --

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

## -- P --

parentChild-class | Classes "parentChild" and "pC"
pC-class | Classes "parentChild" and "pC"
penalise | Class "weightCount"
penalise,weightCount,numeric,numeric-method | Class "weightCount"
phenotype | Class "topGOdata"
phenotype,topGOdata-method | Class "topGOdata"
print,topGOdata-method | Class "topGOdata"
printGenes | Summary for genes annotated to a GO term
printGenes,topGOdata,character,character-method | Summary for genes annotated to a GO term
printGenes,topGOdata,character,missing-method | Summary for genes annotated to a GO term
printGenes-methods | Summary for genes annotated to a GO term
printGraph | ~~ Methods for Function printGraph in Package ‘topGO’ ~~
printGraph,topGOdata,topGOresult,numeric,missing-method | ~~ Methods for Function printGraph in Package ‘topGO’ ~~
printGraph,topGOdata,topGOresult,numeric,topGOresult-method | ~~ Methods for Function printGraph in Package ‘topGO’ ~~
printGraph-methods | ~~ Methods for Function printGraph in Package ‘topGO’ ~~
pType | Class "classicExpr" ~~~
pType,classicExpr-method | Class "classicExpr" ~~~
pType<-,classicExpr-method | Class "classicExpr" ~~~

## -- R --

rankMembers | Class "classicScore"
rankMembers,classicScore-method | Class "classicScore"
rankMembers,elimScore-method | Classes "elimScore" and "removeScore"
rankMembers,removeScore-method | Classes "elimScore" and "removeScore"
removeCount-class | Classes "elimCount" and "removeCount"
removeExpr-class | Class "elimExpr" ~~~
removeScore-class | Classes "elimScore" and "removeScore"
reverseArch | ~~function to do ... ~~
roundFun | Class "weightCount"
roundFun,weightCount-method | Class "weightCount"
runTest | Algorithms for scoring GO terms
runTest,groupStats,missing,missing-method | Class "groupStats"
runTest,groupStats-method | Class "groupStats"
runTest,topGOdata,character,character-method | Algorithms for scoring GO terms
runTest,topGOdata,missing,character-method | Algorithms for scoring GO terms

## -- S --

score | Class "topGOresult"
score,topGOresult-method | Class "topGOresult"
score<-,classicScore-method | Class "classicScore"
score<-,elimScore-method | Classes "elimScore" and "removeScore"
score<-,topGOresult-method | Class "topGOresult"
scoreOrder | Class "classicScore"
scoreOrder,classicScore-method | Class "classicScore"
scoresInTerm | Class "topGOdata"
scoresInTerm,topGOdata,character-method | Class "topGOdata"
scoresInTerm,topGOdata,missing-method | Class "topGOdata"
show,topGOdata-method | Class "topGOdata"
showSigOfNodes | ~~ Methods for Function printGraph in Package ‘topGO’ ~~
sigAllMembers | Class "classicCount"
sigAllMembers,classicCount-method | Class "classicCount"
sigAllMembers,elimCount-method | Classes "elimCount" and "removeCount"
sigAllMembers,parentChild-method | Classes "parentChild" and "pC"
sigAllMembers,removeCount-method | Classes "elimCount" and "removeCount"
sigGenes | Class "topGOdata"
sigGenes,topGOdata-method | Class "topGOdata"
sigMembers | Class "classicCount"
sigMembers,classicCount-method | Class "classicCount"
sigMembers,elimCount-method | Classes "elimCount" and "removeCount"
sigMembers,removeCount-method | Classes "elimCount" and "removeCount"
sigMembers<-,classicCount-method | Class "classicCount"
sigMembers<-,elimCount-method | Classes "elimCount" and "removeCount"
sigMembers<-,parentChild-method | Classes "parentChild" and "pC"
sigMembers<-,pC-method | Classes "parentChild" and "pC"
significant | Class "weightCount"
significant,weightCount-method | Class "weightCount"
sigRatio | Class "weightCount"
sigRatio,weightCount-method | Class "weightCount"
sigRatio<-,weightCount-method | Class "weightCount"

## -- T --

termStat | Class "topGOdata"
termStat,topGOdata,character-method | Class "topGOdata"
termStat,topGOdata,missing-method | Class "topGOdata"
testClass | Class "topGOresult"
testClass,topGOresult-method | Class "topGOresult"
testClass<-,topGOresult-method | Class "topGOresult"
testName | Class "topGOresult"
testName,topGOresult-method | Class "topGOresult"
testName<-,topGOresult-method | Class "topGOresult"
testStatistic | Class "groupStats"
testStatistic,groupStats-method | Class "groupStats"
testStatistic,weightCount-method | Class "weightCount"
testStatPar | Class "groupStats"
testStatPar,groupStats-method | Class "groupStats"
testStatPar,weightCount-method | Class "weightCount"
topGO | Enrichment analysis for Gene Ontology
topGOdata-class | Class "topGOdata"
topGOresult-class | Class "topGOresult"

## -- U --

updateGenes | Class "topGOdata"
updateGenes,topGOdata,factor,missing-method | Class "topGOdata"
updateGenes,topGOdata,numeric,function-method | Class "topGOdata"
updateGroup | Class "groupStats"
updateGroup,groupStats,character,character-method | Class "groupStats"
updateGroup,parentChild,missing,character-method | Classes "parentChild" and "pC"
updateGroup,pC,missing,character-method | Classes "parentChild" and "pC"
updateGroup,pC,missing,missing-method | Classes "parentChild" and "pC"
updateGroup,weightCount,character,character-method | Class "weightCount"
updateTerm<-,topGOdata,character-method | Class "topGOdata"
usedGO | Class "topGOdata"
usedGO,topGOdata-method | Class "topGOdata"

## -- W --

weightCount-class | Class "weightCount"
Weights | Class "weightCount"
Weights,weightCount,logical-method | Class "weightCount"
Weights,weightCount,missing-method | Class "weightCount"
Weights,weightCount-method | Class "weightCount"
Weights<-,weightCount-method | Class "weightCount"
weightScore-class | Class "weightScore" ~~~