topGO: Enrichment analysis for Gene Ontology


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Documentation for package ‘topGO’ version 1.12.0

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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 --

algorithm Class "topGOresult"
algorithm,topGOresult-method Class "topGOresult"
algorithm<- Class "topGOresult"
algorithm<-,topGOresult-method Class "topGOresult"
allGenes Class "topGOdata"
allGenes,topGOdata-method Class "topGOdata"
allMembers Class "groupStats"
allMembers,elimScore-method Classes "elimScore" and "weight01Score"
allMembers,groupStats-method Class "groupStats"
allMembers,parentChild-method Classes "parentChild" and "pC"
allMembers,weight01Expr-method Class "elimExpr" ~~~
allMembers,weight01Score-method Classes "elimScore" and "weight01Score"
allMembers,weightCount-method Class "weightCount"
allMembers<- Class "groupStats"
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 "weight01Score"
allScore,elimScore,missing-method Classes "elimScore" and "weight01Score"
allScore,weight01Score,logical-method Classes "elimScore" and "weight01Score"
allScore,weight01Score,missing-method Classes "elimScore" and "weight01Score"
alternative,elimScore-method Classes "elimScore" and "weight01Score"
annFUN functions to map gene IDs to GO terms
annFUN.db functions to map gene IDs to GO terms
annFUN.file functions to map gene IDs to GO terms
annFUN.gene2GO functions to map gene IDs to GO terms
annFUN.GO2genes functions to map gene IDs to GO terms
annFUN.org 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 --

buildLevels Utility functions for Directed Acyclic Graphs (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 "weight01Count"
countGenesInTerm Class "topGOdata"
countGenesInTerm,topGOdata,character-method Class "topGOdata"
countGenesInTerm,topGOdata,missing-method Class "topGOdata"
cutOff Classes "elimCount" and "weight01Count"
cutOff,elimCount-method Classes "elimCount" and "weight01Count"
cutOff,elimExpr-method Class "elimExpr" ~~~
cutOff,elimScore-method Classes "elimScore" and "weight01Score"
cutOff<- Classes "elimCount" and "weight01Count"
cutOff<-,elimCount-method Classes "elimCount" and "weight01Count"
cutOff<-,elimExpr-method Class "elimExpr" ~~~
cutOff<-,elimScore-method Classes "elimScore" and "weight01Score"

-- D --

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

-- E --

elim Classes "elimCount" and "weight01Count"
elim,elimCount-method Classes "elimCount" and "weight01Count"
elim,elimScore-method Classes "elimScore" and "weight01Score"
elim,weight01Count-method Classes "elimCount" and "weight01Count"
elim,weight01Expr-method Class "elimExpr" ~~~
elim,weight01Score-method Classes "elimScore" and "weight01Score"
elim<- Classes "elimCount" and "weight01Count"
elim<-,elimCount-method Classes "elimCount" and "weight01Count"
elim<-,elimScore-method Classes "elimScore" and "weight01Score"
elim<-,weight01Count-method Classes "elimCount" and "weight01Count"
elim<-,weight01Expr-method Class "elimExpr" ~~~
elim<-,weight01Score-method Classes "elimScore" and "weight01Score"
elimCount-class Classes "elimCount" and "weight01Count"
elimExpr-class Class "elimExpr" ~~~
elimScore-class Classes "elimScore" and "weight01Score"
emptyExpr,classicExpr-method Class "classicExpr" ~~~
expressionMatrix Class "topGOdata"
expressionMatrix,topGOdata-method Class "topGOdata"

-- F --

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

-- G --

geneData Class "topGOresult"
geneData,topGOresult-method Class "topGOresult"
geneData<- Class "topGOresult"
geneData<-,topGOresult-method Class "topGOresult"
geneList A toy example of a list of gene identifiers and the respective p-values
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<- 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 Utility functions for Directed Acyclic Graphs (DAG)
getNoOfLevels Utility functions for Directed Acyclic Graphs (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,weight01Count-method Algorithms for scoring GO terms
getSigGroups,topGOdata,weight01Expr-method Algorithms for scoring GO terms
getSigGroups,topGOdata,weight01Score-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 Gene set tests statistics
GOFisherTest,classicCount-method Class "classicCount"
GOFisherTest,elimCount-method Classes "elimCount" and "weight01Count"
GOglobalTest Gene set tests statistics
GOglobalTest,classicExpr-method Class "classicExpr" ~~~
GOKSTest Gene set tests statistics
GOKSTest,classicScore-method Class "classicScore"
GOKSTest,elimScore-method Classes "elimScore" and "weight01Score"
GOMFTerm ~~function to do ... ~~
GOplot ~~ Methods for Function printGraph in Package 'topGO' ~~
GOtTest Gene set tests statistics
GOtTest,classicScore-method Class "classicScore"
graph Class "topGOdata"
graph,topGOdata-method Class "topGOdata"
graph<- 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 "weight01Count"
initialize,elimExpr-method Class "elimExpr" ~~~
initialize,elimScore-method Classes "elimScore" and "weight01Score"
initialize,groupStats-method Class "groupStats"
initialize,parentChild-method Classes "parentChild" and "pC"
initialize,pC-method Classes "parentChild" and "pC"
initialize,topGOdata-method Class "topGOdata"
initialize,topGOresult-method Class "topGOresult"
initialize,weight01Count-method Classes "elimCount" and "weight01Count"
initialize,weight01Expr-method Class "elimExpr" ~~~
initialize,weight01Score-method Classes "elimScore" and "weight01Score"
initialize,weightCount-method Class "weightCount"
inverseList functions to map gene IDs to GO terms

-- J --

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

-- M --

members Class "groupStats"
members,elimScore-method Classes "elimScore" and "weight01Score"
members,groupStats-method Class "groupStats"
members,weight01Expr-method Class "elimExpr" ~~~
members,weight01Score-method Classes "elimScore" and "weight01Score"
members,weightCount-method Class "weightCount"
members<- Class "groupStats"
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 "weight01Score"
membersScore,weight01Score-method Classes "elimScore" and "weight01Score"

-- N --

Name Class "groupStats"
Name,groupStats-method Class "groupStats"
Name,weightCount-method Class "weightCount"
Name<- Class "groupStats"
Name<-,groupStats-method Class "groupStats"
nodesInInducedGraph ~~function to do ... ~~
numAllMembers Class "groupStats"
numAllMembers,elimCount-method Classes "elimCount" and "weight01Count"
numAllMembers,elimScore-method Classes "elimScore" and "weight01Score"
numAllMembers,groupStats-method Class "groupStats"
numAllMembers,parentChild-method Classes "parentChild" and "pC"
numAllMembers,weight01Count-method Classes "elimCount" and "weight01Count"
numAllMembers,weight01Expr-method Class "elimExpr" ~~~
numAllMembers,weight01Score-method Classes "elimScore" and "weight01Score"
numAllMembers,weightCount-method Class "weightCount"
numGenes Class "topGOdata"
numGenes,topGOdata-method Class "topGOdata"
numMembers Class "groupStats"
numMembers,elimCount-method Classes "elimCount" and "weight01Count"
numMembers,elimScore-method Classes "elimScore" and "weight01Score"
numMembers,groupStats-method Class "groupStats"
numMembers,weight01Count-method Classes "elimCount" and "weight01Count"
numMembers,weight01Expr-method Class "elimExpr" ~~~
numMembers,weight01Score-method Classes "elimScore" and "weight01Score"
numMembers,weightCount-method Class "weightCount"
numSigAll Class "classicCount"
numSigAll,classicCount-method Class "classicCount"
numSigAll,elimCount-method Classes "elimCount" and "weight01Count"
numSigAll,parentChild-method Classes "parentChild" and "pC"
numSigAll,weight01Count-method Classes "elimCount" and "weight01Count"
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 "weight01Count"
numSigMembers,weight01Count-method Classes "elimCount" and "weight01Count"
numSigMembers,weightCount-method Class "weightCount"

-- O --

ontology Class "topGOdata"
ontology,topGOdata-method Class "topGOdata"
ontology<- 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"
print,topGOresult-method Class "topGOresult"
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<- Class "classicExpr" ~~~
pType<-,classicExpr-method Class "classicExpr" ~~~

-- R --

rankMembers Class "classicScore"
rankMembers,classicScore-method Class "classicScore"
rankMembers,elimScore-method Classes "elimScore" and "weight01Score"
rankMembers,weight01Score-method Classes "elimScore" and "weight01Score"
readMappings functions to map gene IDs to GO terms
reverseArch Utility functions for Directed Acyclic Graphs (DAG)
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,character-method Class "topGOresult"
score,topGOresult,missing-method Class "topGOresult"
score<- Class "classicScore"
score<-,classicScore-method Class "classicScore"
score<-,elimScore-method Classes "elimScore" and "weight01Score"
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"
show,topGOresult-method Class "topGOresult"
showGroupDensity ~~ Methods for Function printGraph in Package 'topGO' ~~
showSigOfNodes ~~ Methods for Function printGraph in Package 'topGO' ~~
sigAllMembers Class "classicCount"
sigAllMembers,classicCount-method Class "classicCount"
sigAllMembers,elimCount-method Classes "elimCount" and "weight01Count"
sigAllMembers,parentChild-method Classes "parentChild" and "pC"
sigAllMembers,weight01Count-method Classes "elimCount" and "weight01Count"
sigGenes Class "topGOdata"
sigGenes,topGOdata-method Class "topGOdata"
sigMembers Class "classicCount"
sigMembers,classicCount-method Class "classicCount"
sigMembers,elimCount-method Classes "elimCount" and "weight01Count"
sigMembers,weight01Count-method Classes "elimCount" and "weight01Count"
sigMembers<- Class "classicCount"
sigMembers<-,classicCount-method Class "classicCount"
sigMembers<-,elimCount-method Classes "elimCount" and "weight01Count"
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<- Class "weightCount"
sigRatio<-,weightCount-method Class "weightCount"

-- T --

termStat Class "topGOdata"
termStat,topGOdata,character-method Class "topGOdata"
termStat,topGOdata,missing-method Class "topGOdata"
testName Class "topGOresult"
testName,topGOresult-method Class "topGOresult"
testName<- 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"
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,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<- Class "topGOdata"
updateTerm<-,topGOdata,character-method Class "topGOdata"
usedGO Class "topGOdata"
usedGO,topGOdata-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,weightCount,logical-method Class "weightCount"
Weights,weightCount,missing-method Class "weightCount"
Weights,weightCount-method Class "weightCount"
Weights<- Class "weightCount"
Weights<-,weightCount-method Class "weightCount"
whichAlgorithms Algorithms for scoring GO terms
whichTests Algorithms for scoring GO terms