Enrichment Analysis for Gene Ontology
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Documentation for package ‘topGO’ version 2.60.1
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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 |