Entry: GOFisherTest
Aliases: GOFisherTest
Keywords: misc
Description: Fischer's exact test for gene set
URL: ../../../library/topGO/html/GOFisherTest.html

Entry: GOKSTest
Aliases: GOKSTest GOtTest
Keywords: misc
Description: Kolmogorov-Smirnov test for gene sets
URL: ../../../library/topGO/html/GOKSTest.html

Entry: GOdata
Aliases: GOdata
Keywords: datasets
Description: Example of a topGO data object
URL: ../../../library/topGO/html/GOdata.html

Entry: GOglobalTest
Aliases: GOglobalTest
Keywords: misc
Description: Globaltest for gene sets
URL: ../../../library/topGO/html/GOglobalTest.html

Entry: annFUN
Aliases: annFUN.db annFUN annFUN.GO2genes annFUN.gene2GO
Keywords: misc
Description: functions to map gene IDs to GO terms
URL: ../../../library/topGO/html/annFUN.html

Entry: buildGOgraph.topology
Aliases: buildGOgraph.topology
Keywords: graphs
Description: buils GO graph starting from the most specific GO terms
URL: ../../../library/topGO/html/buildGOgraph.topology.html

Entry: Determines the levels of a Directed Acyclic Graph (DAG)
Aliases: buildLevels getNoOfLevels getGraphRoot
Keywords: graphs
Description: Determines the levels of a Directed Acyclic Graph (DAG)
URL: ../../../library/topGO/html/buildLevels.html

Entry: classicCount-class
Aliases: classicCount-class contTable numSigAll numSigMembers sigAllMembers sigMembers<- sigMembers contTable,classicCount-method initialize,classicCount-method numSigAll,classicCount-method numSigMembers,classicCount-method sigAllMembers,classicCount-method sigMembers<-,classicCount-method sigMembers,classicCount-method GOFisherTest,classicCount-method
Keywords: classes
Description: Class "classicCount"
URL: ../../../library/topGO/html/classicCount-class.html

Entry: classicExpr-class
Aliases: classicExpr-class pType<- pType membersExpr allMembers<-,classicExpr-method emptyExpr,classicExpr-method GOglobalTest,classicExpr-method initialize,classicExpr-method membersExpr,classicExpr-method pType<-,classicExpr-method pType,classicExpr-method
Keywords: classes
Description: Class "classicExpr" ~~~
URL: ../../../library/topGO/html/classicExpr-class.html

Entry: classicScore-class
Aliases: classicScore-class scoreOrder membersScore rankMembers score<- allScore allScore,classicScore,missing-method allScore,classicScore,logical-method scoreOrder,classicScore-method initialize,classicScore-method membersScore,classicScore-method rankMembers,classicScore-method score<-,classicScore-method GOKSTest,classicScore-method GOtTest,classicScore-method
Keywords: classes
Description: Class "classicScore"
URL: ../../../library/topGO/html/classicScore-class.html

Entry: elimCount-class
Aliases: elimCount-class removeCount-class cutOff cutOff,elimCount-method cutOff<- cutOff<-,elimCount-method elim elim,elimCount-method elim,removeCount-method elim<- elim<-,elimCount-method elim<-,removeCount-method initialize,elimCount-method initialize,removeCount-method contTable,elimCount-method numSigAll,elimCount-method numSigMembers,elimCount-method numMembers,elimCount-method numAllMembers,elimCount-method sigAllMembers,elimCount-method sigMembers<-,elimCount-method sigMembers,elimCount-method numAllMembers,removeCount-method numMembers,removeCount-method numSigAll,removeCount-method numSigMembers,removeCount-method sigAllMembers,removeCount-method sigMembers,removeCount-method GOFisherTest,elimCount-method
Keywords: classes
Description: Classes "elimCount" and "removeCount"
URL: ../../../library/topGO/html/elimCount-class.html

Entry: elimExpr-class
Aliases: elimExpr-class removeExpr-class cutOff<-,elimExpr-method cutOff,elimExpr-method initialize,elimExpr-method allMembers,removeExpr-method elim<-,removeExpr-method elim,removeExpr-method initialize,removeExpr-method members,removeExpr-method numAllMembers,removeExpr-method numMembers,removeExpr-method
Keywords: classes
Description: Class "elimExpr" ~~~
URL: ../../../library/topGO/html/elimExpr-class.html

Entry: elimScore-class
Aliases: elimScore-class removeScore-class allMembers,elimScore-method allScore,elimScore,logical-method allScore,elimScore,missing-method cutOff,elimScore-method cutOff<-,elimScore-method elim,elimScore-method elim<-,elimScore-method alternative,elimScore-method GOKSTest,elimScore-method membersScore,elimScore-method members,elimScore-method numMembers,elimScore-method numAllMembers,elimScore-method rankMembers,elimScore-method score<-,elimScore-method initialize,elimScore-method allMembers,removeScore-method allScore,removeScore,missing-method allScore,removeScore,logical-method elim<-,removeScore-method elim,removeScore-method initialize,removeScore-method members,removeScore-method membersScore,removeScore-method numAllMembers,removeScore-method numMembers,removeScore-method rankMembers,removeScore-method
Keywords: classes
Description: Classes "elimScore" and "removeScore"
URL: ../../../library/topGO/html/elimScore-class.html

Entry: getPvalues
Aliases: getPvalues
Keywords: graphs
Description: Function to compute p-values of a t-test for a gene expression matrix.
URL: ../../../library/topGO/html/getPvalues.html

Entry: getSigGroups
Aliases: getSigGroups runTest getSigGroups-methods getSigGroups,topGOdata,classicCount-method getSigGroups,topGOdata,classicScore-method getSigGroups,topGOdata,classicExpr-method getSigGroups,topGOdata,elimCount-method getSigGroups,topGOdata,elimScore-method getSigGroups,topGOdata,elimExpr-method getSigGroups,topGOdata,weightCount-method getSigGroups,topGOdata,removeCount-method getSigGroups,topGOdata,removeScore-method getSigGroups,topGOdata,removeExpr-method getSigGroups,topGOdata,parentChild-method getSigGroups,topGOdata,pC-method runTest,topGOdata,character,character-method runTest,topGOdata,missing,character-method
Keywords: methods
Description: Algorithms for scoring GO terms
URL: ../../../library/topGO/html/getSigGroups.html

Entry: groupGOTerms
Aliases: groupGOTerms GOCCTerm GOBPTerm GOMFTerm
Keywords: misc
Description: ~~function to do ... ~~
URL: ../../../library/topGO/html/groupGOTerms.html

Entry: groupStats-class
Aliases: groupStats-class allMembers<- allMembers members<- members Name<- Name numAllMembers numMembers testStatistic testStatPar updateGroup allMembers<-,groupStats-method allMembers,groupStats-method initialize,groupStats-method members<-,groupStats-method members,groupStats-method Name<-,groupStats-method Name,groupStats-method numAllMembers,groupStats-method numMembers,groupStats-method runTest,groupStats-method runTest,groupStats,missing,missing-method testStatistic,groupStats-method testStatPar,groupStats-method updateGroup,groupStats,character,character-method
Keywords: classes
Description: Class "groupStats"
URL: ../../../library/topGO/html/groupStats-class.html

Entry: inducedGraph
Aliases: inducedGraph
Keywords: graphs
Description: ~~function to do ... ~~
URL: ../../../library/topGO/html/inducedGraph.html

Entry: mapGenes2GOgraph
Aliases: mapGenes2GOgraph
Keywords: graphs
Description: ~~function to do ... ~~
URL: ../../../library/topGO/html/mapGenes2GOgraph.html

Entry: parentChild-class
Aliases: parentChild-class pC-class allParents joinFun allMembers<-,parentChild-method allMembers,parentChild-method allParents,parentChild-method initialize,parentChild-method joinFun,parentChild-method numAllMembers,parentChild-method numSigAll,parentChild-method sigAllMembers,parentChild-method sigMembers<-,parentChild-method updateGroup,parentChild,missing,character-method allMembers<-,pC-method initialize,pC-method sigMembers<-,pC-method updateGroup,pC,missing,character-method updateGroup,pC,missing,missing-method
Keywords: classes
Description: Classes "parentChild" and "pC"
URL: ../../../library/topGO/html/parentChild-class.html

Entry: printGenes-methods
Aliases: printGenes-methods printGenes printGenes,topGOdata,character,character-method printGenes,topGOdata,character,missing-method
Keywords: methods
Description: Summary for genes annotated to a GO term
URL: ../../../library/topGO/html/printGenes-methods.html

Entry: printGraph-methods
Aliases: GOplot showSigOfNodes printGraph-methods printGraph printGraph,topGOdata,topGOresult,numeric,missing-method printGraph,topGOdata,topGOresult,numeric,topGOresult-method
Keywords: methods
Description: ~~ Methods for Function printGraph in Package 'topGO' ~~
URL: ../../../library/topGO/html/printGraph-methods.html

Entry: reverseArch
Aliases: reverseArch
Keywords: graphs
Description: ~~function to do ... ~~
URL: ../../../library/topGO/html/reverseArch.html

Entry: topGO-package
Aliases: topGO-package topGO
Keywords: package
Description: Enrichment analysis for Gene Ontology
URL: ../../../library/topGO/html/topGO-package.html

Entry: topGOdata-class
Aliases: topGOdata-class allGenes attrInTerm countGenesInTerm description<- description feasible<- feasible geneSelectionFun<- geneSelectionFun genes genesInTerm genTable GenTable graph<- graph numGenes ontology<- ontology sigGenes numSigGenes termStat updateGenes updateTerm<- usedGO expressionMatrix phenotype expressionMatrix,topGOdata-method phenotype,topGOdata-method geneScore geneScore,topGOdata,missing-method geneScore,topGOdata,character-method scoresInTerm scoresInTerm,topGOdata,missing-method scoresInTerm,topGOdata,character-method show,topGOdata-method allGenes,topGOdata-method attrInTerm,topGOdata,character,character-method attrInTerm,topGOdata,character,missing-method countGenesInTerm,topGOdata,character-method countGenesInTerm,topGOdata,missing-method description<-,topGOdata,ANY-method description,topGOdata-method feasible<-,topGOdata-method feasible,topGOdata-method geneScore,topGOdata-method geneSelectionFun<-,topGOdata-method geneSelectionFun,topGOdata-method genes,topGOdata-method genesInTerm,topGOdata,character-method genesInTerm,topGOdata,missing-method genTable,topGOdata,list-method GenTable,topGOdata-method graph<-,topGOdata-method graph,topGOdata-method initialize,topGOdata-method numGenes,topGOdata-method ontology<-,topGOdata-method ontology,topGOdata-method print,topGOdata-method sigGenes,topGOdata-method numSigGenes,topGOdata-method termStat,topGOdata,character-method termStat,topGOdata,missing-method updateGenes,topGOdata,numeric,function-method updateGenes,topGOdata,factor,missing-method updateTerm<-,topGOdata,character-method usedGO,topGOdata-method
Keywords: graphs classes
Description: Class "topGOdata"
URL: ../../../library/topGO/html/topGOdata-class.html

Entry: topGOresult-class
Aliases: topGOresult-class description,topGOresult-method description<-,topGOresult,ANY-method testName,topGOresult-method testClass,topGOresult-method testName<-,topGOresult-method testClass<-,topGOresult-method score,topGOresult-method score<-,topGOresult-method initialize,topGOresult-method score testName testClass testName<- testClass<-
Keywords: classes
Description: Class "topGOresult"
URL: ../../../library/topGO/html/topGOresult-class.html

Entry: weightCount-class
Aliases: weightCount-class getSigRatio sigRatio penalise roundFun significant sigRatio<- Weights Weights<- Weights,weightCount-method Weights,weightCount,missing-method Weights,weightCount,logical-method Weights<-,weightCount-method sigRatio,weightCount-method sigRatio<-,weightCount-method penalise,weightCount,numeric,numeric-method roundFun,weightCount-method significant,weightCount-method Name,weightCount-method allMembers,weightCount-method members,weightCount-method testStatistic,weightCount-method testStatPar,weightCount-method updateGroup,weightCount,character,character-method getSigRatio,weightCount-method initialize,weightCount-method numSigAll,weightCount-method numMembers,weightCount-method numSigMembers,weightCount-method numAllMembers,weightCount-method
Keywords: classes
Description: Class "weightCount"
URL: ../../../library/topGO/html/weightCount-class.html

Entry: weightScore-class
Aliases: weightScore-class
Keywords: classes
Description: Class "weightScore" ~~~
URL: ../../../library/topGO/html/weightScore-class.html
