topGO-package	topGO-package
affyLib	geneList
algorithm	topGOresult-class
algorithm,topGOresult-method	topGOresult-class
algorithm<-	topGOresult-class
algorithm<-,topGOresult-method	topGOresult-class
allGenes	topGOdata-class
allGenes,topGOdata-method	topGOdata-class
allMembers	groupStats-class
allMembers,elimScore-method	elimScore-class
allMembers,groupStats-method	groupStats-class
allMembers,parentChild-method	parentChild-class
allMembers,weight01Expr-method	elimExpr-class
allMembers,weight01Score-method	elimScore-class
allMembers,weightCount-method	weightCount-class
allMembers<-	groupStats-class
allMembers<-,classicExpr-method	classicExpr-class
allMembers<-,groupStats-method	groupStats-class
allMembers<-,parentChild-method	parentChild-class
allMembers<-,pC-method	parentChild-class
allParents	parentChild-class
allParents,parentChild-method	parentChild-class
allScore	classicScore-class
allScore,classicScore,logical-method	classicScore-class
allScore,classicScore,missing-method	classicScore-class
allScore,elimScore,logical-method	elimScore-class
allScore,elimScore,missing-method	elimScore-class
allScore,weight01Score,logical-method	elimScore-class
allScore,weight01Score,missing-method	elimScore-class
alternative,elimScore-method	elimScore-class
annFUN	annFUN
annFUN.db	annFUN
annFUN.file	annFUN
annFUN.gene2GO	annFUN
annFUN.GO2genes	annFUN
annFUN.org	annFUN
attrInTerm	topGOdata-class
attrInTerm,topGOdata,character,character-method	topGOdata-class
attrInTerm,topGOdata,character,missing-method	topGOdata-class
buildLevels	dagFunctions
classicCount-class	classicCount-class
classicExpr-class	classicExpr-class
classicScore-class	classicScore-class
combineResults	topGOresult-class
contTable	classicCount-class
contTable,classicCount-method	classicCount-class
contTable,elimCount-method	elimCount-class
countGenesInTerm	topGOdata-class
countGenesInTerm,topGOdata,character-method	topGOdata-class
countGenesInTerm,topGOdata,missing-method	topGOdata-class
cutOff	elimCount-class
cutOff,elimCount-method	elimCount-class
cutOff,elimExpr-method	elimExpr-class
cutOff,elimScore-method	elimScore-class
cutOff<-	elimCount-class
cutOff<-,elimCount-method	elimCount-class
cutOff<-,elimExpr-method	elimExpr-class
cutOff<-,elimScore-method	elimScore-class
depth	elimCount-class
depth,leaCount-method	elimCount-class
depth,leaExpr-method	elimExpr-class
depth,leaScore-method	elimScore-class
depth<-	elimCount-class
depth<-,leaCount-method	elimCount-class
depth<-,leaExpr-method	elimExpr-class
depth<-,leaScore-method	elimScore-class
description	topGOdata-class
description,topGOdata-method	topGOdata-class
description,topGOresult-method	topGOresult-class
description<-	topGOdata-class
description<-,topGOdata,ANY-method	topGOdata-class
description<-,topGOresult,ANY-method	topGOresult-class
elim	elimCount-class
elim,elimCount-method	elimCount-class
elim,elimScore-method	elimScore-class
elim,weight01Count-method	elimCount-class
elim,weight01Expr-method	elimExpr-class
elim,weight01Score-method	elimScore-class
elim<-	elimCount-class
elim<-,elimCount-method	elimCount-class
elim<-,elimScore-method	elimScore-class
elim<-,weight01Count-method	elimCount-class
elim<-,weight01Expr-method	elimExpr-class
elim<-,weight01Score-method	elimScore-class
elimCount-class	elimCount-class
elimExpr-class	elimExpr-class
elimScore-class	elimScore-class
emptyExpr,classicExpr-method	classicExpr-class
expressionMatrix	topGOdata-class
expressionMatrix,topGOdata-method	topGOdata-class
feasible	topGOdata-class
feasible,topGOdata-method	topGOdata-class
feasible<-	topGOdata-class
feasible<-,topGOdata-method	topGOdata-class
geneData	topGOresult-class
geneData,topGOresult-method	topGOresult-class
geneData<-	topGOresult-class
geneData<-,topGOresult-method	topGOresult-class
geneList	geneList
genes	topGOdata-class
genes,topGOdata-method	topGOdata-class
geneScore	topGOdata-class
geneScore,topGOdata,character-method	topGOdata-class
geneScore,topGOdata,missing-method	topGOdata-class
geneScore,topGOdata-method	topGOdata-class
geneSelectionFun	topGOdata-class
geneSelectionFun,topGOdata-method	topGOdata-class
geneSelectionFun<-	topGOdata-class
geneSelectionFun<-,topGOdata-method	topGOdata-class
genesInTerm	topGOdata-class
genesInTerm,topGOdata,character-method	topGOdata-class
genesInTerm,topGOdata,missing-method	topGOdata-class
GenTable	diagnosticMethods
GenTable,topGOdata-method	diagnosticMethods
getGraphRoot	dagFunctions
getNoOfLevels	dagFunctions
getPvalues	getPvalues
getSigGroups	getSigGroups
getSigGroups,topGOdata,classicCount-method	getSigGroups
getSigGroups,topGOdata,classicExpr-method	getSigGroups
getSigGroups,topGOdata,classicScore-method	getSigGroups
getSigGroups,topGOdata,elimCount-method	getSigGroups
getSigGroups,topGOdata,elimExpr-method	getSigGroups
getSigGroups,topGOdata,elimScore-method	getSigGroups
getSigGroups,topGOdata,leaCount-method	getSigGroups
getSigGroups,topGOdata,leaExpr-method	getSigGroups
getSigGroups,topGOdata,leaScore-method	getSigGroups
getSigGroups,topGOdata,parentChild-method	getSigGroups
getSigGroups,topGOdata,pC-method	getSigGroups
getSigGroups,topGOdata,weight01Count-method	getSigGroups
getSigGroups,topGOdata,weight01Expr-method	getSigGroups
getSigGroups,topGOdata,weight01Score-method	getSigGroups
getSigGroups,topGOdata,weightCount-method	getSigGroups
getSigGroups-methods	getSigGroups
getSigRatio	weightCount-class
getSigRatio,weightCount-method	weightCount-class
GOBPTerm	groupGOTerms
GOCCTerm	groupGOTerms
GOdata	GOdata
GOFisherTest	GOTests
GOFisherTest,classicCount-method	classicCount-class
GOFisherTest,elimCount-method	elimCount-class
GOglobalTest	GOTests
GOglobalTest,classicExpr-method	classicExpr-class
GOKSTest	GOTests
GOKSTest,classicScore-method	classicScore-class
GOKSTiesTest	GOTests
GOKSTiesTest,classicScore-method	classicScore-class
GOMFTerm	groupGOTerms
GOplot	printGraph-methods
GOSumTest	GOTests
GOSumTest,classicScore-method	classicScore-class
GOtTest	GOTests
GOtTest,classicScore-method	classicScore-class
graph	topGOdata-class
graph,topGOdata-method	topGOdata-class
graph<-	topGOdata-class
graph<-,topGOdata-method	topGOdata-class
groupGOTerms	groupGOTerms
groupStats-class	groupStats-class
inducedGraph	inducedGraph
initialize,classicCount-method	classicCount-class
initialize,classicExpr-method	classicExpr-class
initialize,classicScore-method	classicScore-class
initialize,elimCount-method	elimCount-class
initialize,elimExpr-method	elimExpr-class
initialize,elimScore-method	elimScore-class
initialize,groupStats-method	groupStats-class
initialize,leaCount-method	elimCount-class
initialize,leaExpr-method	elimExpr-class
initialize,leaScore-method	elimScore-class
initialize,parentChild-method	parentChild-class
initialize,pC-method	parentChild-class
initialize,topGOdata-method	topGOdata-class
initialize,topGOresult-method	topGOresult-class
initialize,weight01Count-method	elimCount-class
initialize,weight01Expr-method	elimExpr-class
initialize,weight01Score-method	elimScore-class
initialize,weightCount-method	weightCount-class
inverseList	annFUN
joinFun	parentChild-class
joinFun,parentChild-method	parentChild-class
leaCount-class	elimCount-class
leaExpr-class	elimExpr-class
leaScore-class	elimScore-class
members	groupStats-class
members,elimScore-method	elimScore-class
members,groupStats-method	groupStats-class
members,weight01Expr-method	elimExpr-class
members,weight01Score-method	elimScore-class
members,weightCount-method	weightCount-class
members<-	groupStats-class
members<-,groupStats-method	groupStats-class
membersExpr	classicExpr-class
membersExpr,classicExpr-method	classicExpr-class
membersScore	classicScore-class
membersScore,classicScore-method	classicScore-class
membersScore,elimScore-method	elimScore-class
membersScore,weight01Score-method	elimScore-class
Name	groupStats-class
Name,groupStats-method	groupStats-class
Name,weightCount-method	weightCount-class
Name<-	groupStats-class
Name<-,groupStats-method	groupStats-class
nodesInInducedGraph	inducedGraph
numAllMembers	groupStats-class
numAllMembers,elimCount-method	elimCount-class
numAllMembers,elimScore-method	elimScore-class
numAllMembers,groupStats-method	groupStats-class
numAllMembers,parentChild-method	parentChild-class
numAllMembers,weight01Count-method	elimCount-class
numAllMembers,weight01Expr-method	elimExpr-class
numAllMembers,weight01Score-method	elimScore-class
numAllMembers,weightCount-method	weightCount-class
numGenes	topGOdata-class
numGenes,topGOdata-method	topGOdata-class
numMembers	groupStats-class
numMembers,elimCount-method	elimCount-class
numMembers,elimScore-method	elimScore-class
numMembers,groupStats-method	groupStats-class
numMembers,weight01Count-method	elimCount-class
numMembers,weight01Expr-method	elimExpr-class
numMembers,weight01Score-method	elimScore-class
numMembers,weightCount-method	weightCount-class
numSigAll	classicCount-class
numSigAll,classicCount-method	classicCount-class
numSigAll,elimCount-method	elimCount-class
numSigAll,parentChild-method	parentChild-class
numSigAll,weight01Count-method	elimCount-class
numSigAll,weightCount-method	weightCount-class
numSigGenes	topGOdata-class
numSigGenes,topGOdata-method	topGOdata-class
numSigMembers	classicCount-class
numSigMembers,classicCount-method	classicCount-class
numSigMembers,elimCount-method	elimCount-class
numSigMembers,weight01Count-method	elimCount-class
numSigMembers,weightCount-method	weightCount-class
ontology	topGOdata-class
ontology,topGOdata-method	topGOdata-class
ontology<-	topGOdata-class
ontology<-,topGOdata-method	topGOdata-class
parentChild-class	parentChild-class
pC-class	parentChild-class
penalise	weightCount-class
penalise,weightCount,numeric,numeric-method	weightCount-class
permSumStats	GOTests
permSumStats.all	GOTests
phenotype	topGOdata-class
phenotype,topGOdata-method	topGOdata-class
print,topGOdata-method	topGOdata-class
print,topGOresult-method	topGOresult-class
printGenes	diagnosticMethods
printGenes,topGOdata,character,character-method	diagnosticMethods
printGenes,topGOdata,character,missing-method	diagnosticMethods
printGenes-methods	diagnosticMethods
printGraph	printGraph-methods
printGraph,topGOdata,topGOresult,numeric,missing-method	printGraph-methods
printGraph,topGOdata,topGOresult,numeric,topGOresult-method	printGraph-methods
printGraph-methods	printGraph-methods
pType	classicExpr-class
pType,classicExpr-method	classicExpr-class
pType<-	classicExpr-class
pType<-,classicExpr-method	classicExpr-class
rankMembers	classicScore-class
rankMembers,classicScore-method	classicScore-class
rankMembers,elimScore-method	elimScore-class
rankMembers,weight01Score-method	elimScore-class
readMappings	annFUN
resultFisher	GOdata
resultKS	GOdata
reverseArch	dagFunctions
roundFun	weightCount-class
roundFun,weightCount-method	weightCount-class
runTest	getSigGroups
runTest,groupStats,missing,missing-method	groupStats-class
runTest,groupStats-method	groupStats-class
runTest,topGOdata,character,character-method	getSigGroups
runTest,topGOdata,missing,character-method	getSigGroups
score	topGOresult-class
score,topGOresult,character-method	topGOresult-class
score,topGOresult,missing-method	topGOresult-class
score<-	classicScore-class
score<-,classicScore-method	classicScore-class
score<-,elimScore-method	elimScore-class
score<-,topGOresult-method	topGOresult-class
scoreOrder	classicScore-class
scoreOrder,classicScore-method	classicScore-class
scoresInTerm	topGOdata-class
scoresInTerm,topGOdata,character-method	topGOdata-class
scoresInTerm,topGOdata,missing-method	topGOdata-class
show,topGOdata-method	topGOdata-class
show,topGOresult-method	topGOresult-class
showGroupDensity	diagnosticMethods
showSigOfNodes	printGraph-methods
sigAllMembers	classicCount-class
sigAllMembers,classicCount-method	classicCount-class
sigAllMembers,elimCount-method	elimCount-class
sigAllMembers,parentChild-method	parentChild-class
sigAllMembers,weight01Count-method	elimCount-class
sigGenes	topGOdata-class
sigGenes,topGOdata-method	topGOdata-class
sigMembers	classicCount-class
sigMembers,classicCount-method	classicCount-class
sigMembers,elimCount-method	elimCount-class
sigMembers,weight01Count-method	elimCount-class
sigMembers<-	classicCount-class
sigMembers<-,classicCount-method	classicCount-class
sigMembers<-,elimCount-method	elimCount-class
sigMembers<-,parentChild-method	parentChild-class
sigMembers<-,pC-method	parentChild-class
significant	weightCount-class
significant,weightCount-method	weightCount-class
sigRatio	weightCount-class
sigRatio,weightCount-method	weightCount-class
sigRatio<-	weightCount-class
sigRatio<-,weightCount-method	weightCount-class
termStat	topGOdata-class
termStat,topGOdata,character-method	topGOdata-class
termStat,topGOdata,missing-method	topGOdata-class
testName	topGOresult-class
testName,topGOresult-method	topGOresult-class
testName<-	topGOresult-class
testName<-,topGOresult-method	topGOresult-class
testStatistic	groupStats-class
testStatistic,groupStats-method	groupStats-class
testStatistic,weightCount-method	weightCount-class
testStatPar	groupStats-class
testStatPar,groupStats-method	groupStats-class
testStatPar,weightCount-method	weightCount-class
topDiffGenes	geneList
topGO	topGO-package
topGOdata-class	topGOdata-class
topGOresult-class	topGOresult-class
updateGenes	topGOdata-class
updateGenes,topGOdata,factor,missing-method	topGOdata-class
updateGenes,topGOdata,numeric,function-method	topGOdata-class
updateGroup	groupStats-class
updateGroup,groupStats,character,character-method	groupStats-class
updateGroup,parentChild,missing,character-method	parentChild-class
updateGroup,pC,missing,character-method	parentChild-class
updateGroup,pC,missing,missing-method	parentChild-class
updateGroup,weightCount,character,character-method	weightCount-class
updateTerm<-	topGOdata-class
updateTerm<-,topGOdata,character-method	topGOdata-class
usedGO	topGOdata-class
usedGO,topGOdata-method	topGOdata-class
weight01Count-class	elimCount-class
weight01Expr-class	elimExpr-class
weight01Score-class	elimScore-class
weightCount-class	weightCount-class
Weights	weightCount-class
Weights,weightCount,logical-method	weightCount-class
Weights,weightCount,missing-method	weightCount-class
Weights,weightCount-method	weightCount-class
Weights<-	weightCount-class
Weights<-,weightCount-method	weightCount-class
whichAlgorithms	getSigGroups
whichTests	getSigGroups
