Package: topGO 2.59.0

Adrian Alexa

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:Adrian Alexa, Jorg Rahnenfuhrer

topGO_2.59.0.tar.gz
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topGO.pdf |topGO.html✨
topGO/json (API)

# Install 'topGO' in R:

install.packages('topGO', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

GOdata - Sample topGOdata and topGOresult objects
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
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-2.59.0(bioc 3.21)topGO-2.58.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarray visualization

8.91 score 20 packages 1.7k scripts 3.9k downloads 652 mentions 111 exports 44 dependencies

Last updated 23 days agofrom:2711dac851. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 18 2024
R-4.5-win	NOTE	Nov 18 2024
R-4.5-linux	NOTE	Nov 18 2024
R-4.4-win	NOTE	Nov 18 2024
R-4.4-mac	NOTE	Nov 18 2024
R-4.3-win	NOTE	Nov 18 2024
R-4.3-mac	NOTE	Nov 18 2024

Exports:.countsInNode .genesInNode algorithm algorithm<-allGenes allMembers allMembers<-allParents allScore annFUN annFUN.db annFUN.file annFUN.gene2GO annFUN.GO2genes annFUN.org attrInTerm buildLevels combineResults contTable countGenesInTerm cutOff cutOff<-depth depth<-description description<-elim elim<-expressionMatrix feasible feasible<-geneData geneData<-genes geneScore geneSelectionFun geneSelectionFun<-genesInTerm GenTable getGraphRoot getNoOfLevels getPvalues getSigGroups getSigRatio GOFisherTest GOglobalTest GOKSTest GOKSTiesTest GOplot GOSumTest GOtTest graph graph<-groupGOTerms inducedGraph initialize inverseList joinFun members members<-membersExpr membersScore Name Name<-nodesInInducedGraph numAllMembers numGenes numMembers numSigAll numSigGenes numSigMembers ontology ontology<-penalise permSumStats permSumStats.all phenotype print printGenes printGraph pType pType<-rankMembers readMappings reverseArch runTest score score<-scoreOrder scoresInTerm show showGroupDensity showSigOfNodes sigAllMembers sigGenes sigMembers sigMembers<-sigRatio<-termStat testName testName<-testStatistic testStatPar updateGenes updateGroup updateTerm<-usedGO Weights Weights<-whichAlgorithms whichTests

Dependencies:AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI fastmap generics GenomeInfoDb GenomeInfoDbData glue GO.db graph httr IRanges jsonlite KEGGREST lattice lifecycle matrixStats memoise mime openssl pkgconfig plogr png R6 rlang RSQLite S4Vectors SparseM sys UCSC.utils vctrs XVector zlibbioc

topGO

Rendered fromtopGO.Rnwusingutils::Sweaveon Nov 18 2024.

Last update: 2019-12-10
Started: 2013-11-01

Citation

Development and contributors

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