Introduction | Installation | Quick start guide | Data preparation | Performing the enrichment tests | Analysis of results | The gene universe and the set of interesting genes | The topGOdata object | Custom annotations | Predefined list of interesting genes | Using the genes score | Filtering and missing GO annotations | Working with the topGOdata object | Running the enrichment tests | Defining and running the test | The groupStats classes | Performing the test | The adjustment of $p$-values | runTest: a high-level interface for testing | Interpretation and visualization of results | The topGOresult object | Summarising the results | Analysing individual GOs | Visualising the GO structure | Session Information | References
Package: topGO 2.65.0
Federico Marini
topGO: Enrichment Analysis for Gene Ontology
topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.
Authors:
topGO_2.65.0.tar.gz
topGO_2.65.0.zip(r-4.7)topGO_2.65.0.zip(r-4.6)topGO_2.65.0.zip(r-4.5)
topGO_2.65.0.tgz(r-4.6-any)topGO_2.65.0.tgz(r-4.5-any)
topGO_2.65.0.tar.gz(r-4.7-any)topGO_2.65.0.tar.gz(r-4.6-any)
topGO_2.65.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
topGO/json (API)
| # Install 'topGO' in R: |
| install.packages('topGO', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/federicomarini/topgo/issues
Datasets:
- affyLib - A toy example of a list of gene identifiers and the respective p-values
- geneList - A toy example of a list of gene identifiers and the respective p-values
- GOdata - Sample topGOdata and topGOresult objects
- resultFisher - Sample topGOdata and topGOresult objects
- resultKS - Sample topGOdata and topGOresult objects
- topDiffGenes - A toy example of a list of gene identifiers and the respective p-values
On BioConductor:topGO-2.65.0(bioc 3.24)topGO-2.64.0(bioc 3.23)
geneexpressiontranscriptomicsgenesetenrichmentgoannotationpathwayssystemsbiologymicroarraysequencingvisualizationsoftware
Last updated from:b30d41d2b8. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 219 | ||
| linux-devel-x86_64 | WARNING | 278 | ||
| source / vignettes | OK | 372 | ||
| linux-release-x86_64 | WARNING | 318 | ||
| macos-release-arm64 | WARNING | 257 | ||
| macos-oldrel-arm64 | WARNING | 141 | ||
| windows-devel | WARNING | 192 | ||
| windows-release | WARNING | 203 | ||
| windows-oldrel | WARNING | 201 | ||
| wasm-release | OK | 165 |
Exports:.countsInNode.genesInNodealgorithmalgorithm<-allGenesallMembersallMembers<-allParentsallScoreannFUNannFUN.dbannFUN.fileannFUN.gene2GOannFUN.GO2genesannFUN.orgattrInTermbuildLevelscombineResultscontTablecountGenesInTermcutOffcutOff<-depthdepth<-descriptiondescription<-elimelim<-expressionMatrixfeasiblefeasible<-geneDatageneData<-genesgeneScoregeneSelectionFungeneSelectionFun<-genesInTermGenTablegetGraphRootgetNoOfLevelsgetPvaluesgetSigGroupsgetSigRatioGOFisherTestGOglobalTestGOKSTestGOKSTiesTestGOplotGOSumTestGOtTestgraphgraph<-groupGOTermsinducedGraphinitializeinverseListjoinFunmembersmembers<-membersExprmembersScoreNameName<-nodesInInducedGraphnumAllMembersnumGenesnumMembersnumSigAllnumSigGenesnumSigMembersontologyontology<-penalisepermSumStatspermSumStats.allphenotypeprintprintGenesprintGraphpTypepType<-rankMembersreadMappingsreverseArchrunTestscorescore<-scoreOrderscoresInTermshowshowGroupDensityshowSigOfNodessigAllMemberssigGenessigMemberssigMembers<-sigRatio<-termStattestNametestName<-testStatistictestStatParupdateGenesupdateGroupupdateTerm<-usedGOWeightsWeights<-whichAlgorithmswhichTests
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapgenericsglueGO.dbgraphhttrIRangesjsonliteKEGGRESTlatticelifecyclematrixStatsmemoisemimeopensslpkgconfigpngR6rlangRSQLiteS4VectorsSeqinfoSparseMsysvctrsXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Enrichment analysis for Gene Ontology | topGO-package topGO |
| Functions which map gene identifiers to GO terms | annFUN annFUN.db annFUN.file annFUN.gene2GO annFUN.GO2genes annFUN.org inverseList readMappings |
| Class "classicCount" | classicCount-class contTable contTable,classicCount-method GOFisherTest,classicCount-method initialize,classicCount-method numSigAll numSigAll,classicCount-method numSigMembers numSigMembers,classicCount-method sigAllMembers sigAllMembers,classicCount-method sigMembers sigMembers,classicCount-method sigMembers<- sigMembers<-,classicCount-method |
| Class "classicExpr" | allMembers<-,classicExpr-method classicExpr-class emptyExpr,classicExpr-method GOglobalTest,classicExpr-method initialize,classicExpr-method membersExpr membersExpr,classicExpr-method pType pType,classicExpr-method pType<- pType<-,classicExpr-method |
| Class "classicScore" | allScore allScore,classicScore,logical-method allScore,classicScore,missing-method classicScore-class GOKSTest,classicScore-method GOKSTiesTest,classicScore-method GOSumTest,classicScore-method GOtTest,classicScore-method initialize,classicScore-method membersScore membersScore,classicScore-method rankMembers rankMembers,classicScore-method score<- score<-,classicScore-method scoreOrder scoreOrder,classicScore-method |
| Utility functions to work with Directed Acyclic Graphs (DAG) | buildLevels getGraphRoot getNoOfLevels reverseArch |
| Diagnostic functions for topGOdata and topGOresult objects. | GenTable GenTable,topGOdata-method printGenes printGenes,topGOdata,character,character-method printGenes,topGOdata,character,missing-method printGenes-methods showGroupDensity |
| Classes "elimCount" and "weight01Count" | contTable,elimCount-method cutOff cutOff,elimCount-method cutOff<- cutOff<-,elimCount-method depth depth,leaCount-method depth<- depth<-,leaCount-method elim elim,elimCount-method elim,weight01Count-method elim<- elim<-,elimCount-method elim<-,weight01Count-method elimCount-class GOFisherTest,elimCount-method initialize,elimCount-method initialize,leaCount-method initialize,weight01Count-method leaCount-class numAllMembers,elimCount-method numAllMembers,weight01Count-method numMembers,elimCount-method numMembers,weight01Count-method numSigAll,elimCount-method numSigAll,weight01Count-method numSigMembers,elimCount-method numSigMembers,weight01Count-method sigAllMembers,elimCount-method sigAllMembers,weight01Count-method sigMembers,elimCount-method sigMembers,weight01Count-method sigMembers<-,elimCount-method weight01Count-class |
| Class "elimExpr" | allMembers,weight01Expr-method cutOff,elimExpr-method cutOff<-,elimExpr-method depth,leaExpr-method depth<-,leaExpr-method elim,weight01Expr-method elim<-,weight01Expr-method elimExpr-class initialize,elimExpr-method initialize,leaExpr-method initialize,weight01Expr-method leaExpr-class members,weight01Expr,missing-method numAllMembers,weight01Expr-method numMembers,weight01Expr-method weight01Expr-class |
| Classes "elimScore" and "weight01Score" | allMembers,elimScore-method allMembers,weight01Score-method allScore,elimScore,logical-method allScore,elimScore,missing-method allScore,weight01Score,logical-method allScore,weight01Score,missing-method alternative,elimScore-method cutOff,elimScore-method cutOff<-,elimScore-method depth,leaScore-method depth<-,leaScore-method elim,elimScore-method elim,weight01Score-method elim<-,elimScore-method elim<-,weight01Score-method elimScore-class initialize,elimScore-method initialize,leaScore-method initialize,weight01Score-method leaScore-class members,elimScore-method members,weight01Score,missing-method membersScore,elimScore-method membersScore,weight01Score-method numAllMembers,elimScore-method numAllMembers,weight01Score-method numMembers,elimScore-method numMembers,weight01Score-method rankMembers,elimScore-method rankMembers,weight01Score-method score<-,elimScore-method weight01Score-class |
| Gene set tests statistics | GOFisherTest GOglobalTest GOKSTest GOKSTiesTest GOSumTest GOtTest permSumStats permSumStats.all |
| A toy example of a list of gene identifiers and the respective p-values | affyLib geneList topDiffGenes |
| Convenient function to compute p-values from a gene expression matrix. | getPvalues |
| Interfaces for running the enrichment tests | getSigGroups getSigGroups,topGOdata,classicCount-method getSigGroups,topGOdata,classicExpr-method getSigGroups,topGOdata,classicScore-method getSigGroups,topGOdata,elimCount-method getSigGroups,topGOdata,elimExpr-method getSigGroups,topGOdata,elimScore-method getSigGroups,topGOdata,leaCount-method getSigGroups,topGOdata,leaExpr-method getSigGroups,topGOdata,leaScore-method getSigGroups,topGOdata,parentChild-method getSigGroups,topGOdata,pC-method getSigGroups,topGOdata,weight01Count-method getSigGroups,topGOdata,weight01Expr-method getSigGroups,topGOdata,weight01Score-method getSigGroups,topGOdata,weightCount-method getSigGroups-methods runTest runTest,topGOdata,character,character-method runTest,topGOdata,missing,character-method whichAlgorithms whichTests |
| Sample topGOdata and topGOresult objects | GOdata resultFisher resultKS |
| Grouping of GO terms into the three ontologies | GOBPTerm GOCCTerm GOMFTerm groupGOTerms |
| Class "groupStats" | allMembers allMembers,groupStats-method allMembers<- allMembers<-,groupStats-method groupStats-class initialize,groupStats-method members members,groupStats,missing-method members<- members<-,groupStats-method Name Name,groupStats-method Name<- Name<-,groupStats-method numAllMembers numAllMembers,groupStats-method numMembers numMembers,groupStats-method runTest,groupStats,missing,missing-method runTest,groupStats-method testStatistic testStatistic,groupStats-method testStatPar testStatPar,groupStats-method updateGroup updateGroup,groupStats,character,character-method |
| The subgraph induced by a set of nodes. | inducedGraph nodesInInducedGraph |
| Classes "parentChild" and "pC" | allMembers,parentChild-method allMembers<-,parentChild-method allMembers<-,pC-method allParents allParents,parentChild-method initialize,parentChild-method initialize,pC-method joinFun joinFun,parentChild-method numAllMembers,parentChild-method numSigAll,parentChild-method parentChild-class pC-class sigAllMembers,parentChild-method sigMembers<-,parentChild-method sigMembers<-,pC-method updateGroup,parentChild,missing,character-method updateGroup,pC,missing,character-method updateGroup,pC,missing,missing-method |
| Visualisation functions | GOplot printGraph printGraph,topGOdata,topGOresult,numeric,missing-method printGraph,topGOdata,topGOresult,numeric,topGOresult-method printGraph-methods showSigOfNodes |
| Class "topGOdata" | allGenes allGenes,topGOdata-method attrInTerm attrInTerm,topGOdata,character,character-method attrInTerm,topGOdata,character,missing-method countGenesInTerm countGenesInTerm,topGOdata,character-method countGenesInTerm,topGOdata,missing-method description description,topGOdata-method description<- description<-,topGOdata,ANY-method expressionMatrix expressionMatrix,topGOdata-method feasible feasible,topGOdata-method feasible<- feasible<-,topGOdata-method genes genes,topGOdata-method geneScore geneScore,topGOdata,character-method geneScore,topGOdata,missing-method geneScore,topGOdata-method geneSelectionFun geneSelectionFun,topGOdata-method geneSelectionFun<- geneSelectionFun<-,topGOdata-method genesInTerm genesInTerm,topGOdata,character-method genesInTerm,topGOdata,missing-method graph graph,topGOdata-method graph<- graph<-,topGOdata-method initialize,topGOdata-method numGenes numGenes,topGOdata-method numSigGenes numSigGenes,topGOdata-method ontology ontology,topGOdata-method ontology<- ontology<-,topGOdata-method phenotype phenotype,topGOdata-method print,topGOdata-method scoresInTerm scoresInTerm,topGOdata,character-method scoresInTerm,topGOdata,missing-method show,topGOdata-method sigGenes sigGenes,topGOdata-method termStat termStat,topGOdata,character-method termStat,topGOdata,missing-method topGOdata-class updateGenes updateGenes,topGOdata,factor,missing-method updateGenes,topGOdata,numeric,function-method updateTerm<- updateTerm<-,topGOdata,character-method usedGO usedGO,topGOdata-method |
| Class "topGOresult" | algorithm algorithm,topGOresult-method algorithm<- algorithm<-,topGOresult-method combineResults description,topGOresult-method description<-,topGOresult,ANY-method geneData geneData,topGOresult-method geneData<- geneData<-,topGOresult-method initialize,topGOresult-method print,topGOresult-method score score,topGOresult-method score<-,topGOresult-method show,topGOresult-method testName testName,topGOresult-method testName<- testName<-,topGOresult-method topGOresult-class |
| Class "weightCount" | allMembers,weightCount-method getSigRatio getSigRatio,weightCount-method initialize,weightCount-method members,weightCount-method Name,weightCount-method numAllMembers,weightCount-method numMembers,weightCount-method numSigAll,weightCount-method numSigMembers,weightCount-method penalise penalise,weightCount,numeric,numeric-method roundFun roundFun,weightCount-method significant significant,weightCount-method sigRatio sigRatio,weightCount-method sigRatio<- sigRatio<-,weightCount-method testStatistic,weightCount-method testStatPar,weightCount-method updateGroup,weightCount,character,character-method weightCount-class Weights Weights,weightCount,logical-method Weights,weightCount,missing-method Weights,weightCount-method Weights<- Weights<-,weightCount-method |
