topGO: Enrichment Analysis for Gene Ontology
Version 2.28.0

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.

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AuthorAdrian Alexa, Jorg Rahnenfuhrer
Bioconductor views Microarray Visualization
Date of publicationNone
MaintainerAdrian Alexa <adrian.alexa@gmail.com>
LicenseLGPL
Version2.28.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("topGO")

Man pages

annFUN: Functions which map gene identifiers to GO terms
classicCount-class: Class "classicCount"
classicExpr-class: Class "classicExpr"
classicScore-class: Class "classicScore"
dagFunctions: Utility functions to work with Directed Acyclic Graphs (DAG)
diagnosticMethods: Diagnostic functions for topGOdata and topGOresult objects.
elimCount-class: Classes "elimCount" and "weight01Count"
elimExpr-class: Class "elimExpr"
elimScore-class: Classes "elimScore" and "weight01Score"
geneList: A toy example of a list of gene identifiers and the...
getPvalues: Convenient function to compute p-values from a gene...
getSigGroups: Interfaces for running the enrichment tests
GOdata: Sample topGOdata and topGOresult objects
GOTests: Gene set tests statistics
groupGOTerms: Grouping of GO terms into the three ontologies
groupStats-class: Class "groupStats"
inducedGraph: The subgraph induced by a set of nodes.
parentChild-class: Classes "parentChild" and "pC"
printGraph-methods: Visualisation functions
topGOdata-class: Class "topGOdata"
topGO-package: Enrichment analysis for Gene Ontology
topGOresult-class: Class "topGOresult"
weightCount-class: Class "weightCount"

Functions

GOBPTerm Man page
GOCCTerm Man page
GOFisherTest Man page
GOFisherTest,classicCount-method Man page
GOFisherTest,elimCount-method Man page
GOKSTest Man page
GOKSTest,classicScore-method Man page
GOKSTiesTest Man page
GOKSTiesTest,classicScore-method Man page
GOMFTerm Man page
GOSumTest Man page
GOSumTest,classicScore-method Man page
GOdata Man page
GOglobalTest Man page
GOglobalTest,classicExpr-method Man page
GOplot Man page Source code
GOplot.counts Source code
GOtTest Man page
GOtTest,classicScore-method Man page
GenTable Man page
GenTable,topGOdata-method Man page
Name Man page
Name,groupStats-method Man page
Name,weightCount-method Man page
Name<- Man page
Name<-,groupStats-method Man page
Weights Man page
Weights,weightCount,logical-method Man page
Weights,weightCount,missing-method Man page
Weights,weightCount-method Man page
Weights<- Man page
Weights<-,weightCount-method Man page
affyLib Man page
algorithm Man page
algorithm,topGOresult-method Man page
algorithm<- Man page
algorithm<-,topGOresult-method Man page
allGenes Man page
allGenes,topGOdata-method Man page
allMembers Man page
allMembers,elimScore-method Man page
allMembers,groupStats-method Man page
allMembers,parentChild-method Man page
allMembers,weight01Expr-method Man page
allMembers,weight01Score-method Man page
allMembers,weightCount-method Man page
allMembers<- Man page
allMembers<-,classicExpr-method Man page
allMembers<-,groupStats-method Man page
allMembers<-,pC-method Man page
allMembers<-,parentChild-method Man page
allParents Man page
allParents,parentChild-method Man page
allScore Man page
allScore,classicScore,logical-method Man page
allScore,classicScore,missing-method Man page
allScore,elimScore,logical-method Man page
allScore,elimScore,missing-method Man page
allScore,weight01Score,logical-method Man page
allScore,weight01Score,missing-method Man page
alternative,elimScore-method Man page
annFUN Man page Source code
annFUN.GO2genes Man page Source code
annFUN.db Man page Source code
annFUN.file Man page Source code
annFUN.gene2GO Man page Source code
annFUN.org Man page Source code
attrInTerm Man page
attrInTerm,topGOdata,character,character-method Man page
attrInTerm,topGOdata,character,missing-method Man page
buildGOgraph.topology Source code
buildLevels Man page Source code
classicCount-class Man page
classicExpr-class Man page
classicScore-class Man page
combineResults Man page Source code
contTable Man page
contTable,classicCount-method Man page
contTable,elimCount-method Man page
countGenesInTerm Man page
countGenesInTerm,topGOdata,character-method Man page
countGenesInTerm,topGOdata,missing-method Man page
countsInNode Source code
cutOff Man page
cutOff,elimCount-method Man page
cutOff,elimExpr-method Man page
cutOff,elimScore-method Man page
cutOff<- Man page
cutOff<-,elimCount-method Man page
cutOff<-,elimExpr-method Man page
cutOff<-,elimScore-method Man page
depth Man page
depth,leaCount-method Man page
depth,leaExpr-method Man page
depth,leaScore-method Man page
depth<- Man page
depth<-,leaCount-method Man page
depth<-,leaExpr-method Man page
depth<-,leaScore-method Man page
description Man page
description,topGOdata-method Man page
description,topGOresult-method Man page
description<- Man page
description<-,topGOdata,ANY-method Man page
description<-,topGOresult,ANY-method Man page
elim Man page
elim,elimCount-method Man page
elim,elimScore-method Man page
elim,weight01Count-method Man page
elim,weight01Expr-method Man page
elim,weight01Score-method Man page
elim<- Man page
elim<-,elimCount-method Man page
elim<-,elimScore-method Man page
elim<-,weight01Count-method Man page
elim<-,weight01Expr-method Man page
elim<-,weight01Score-method Man page
elimCount-class Man page
elimExpr-class Man page
elimScore-class Man page
emptyExpr,classicExpr-method Man page
expressionMatrix Man page
expressionMatrix,topGOdata-method Man page
feasible Man page
feasible,topGOdata-method Man page
feasible<- Man page
feasible<-,topGOdata-method Man page
feasibleGenes.db Source code
geneData Man page
geneData,topGOresult-method Man page
geneData<- Man page
geneData<-,topGOresult-method Man page
geneList Man page
geneScore Man page
geneScore,topGOdata,character-method Man page
geneScore,topGOdata,missing-method Man page
geneScore,topGOdata-method Man page
geneSelectionFun Man page
geneSelectionFun,topGOdata-method Man page
geneSelectionFun<- Man page
geneSelectionFun<-,topGOdata-method Man page
genes Man page
genes,topGOdata-method Man page
genesInNode Source code
genesInTerm Man page
genesInTerm,topGOdata,character-method Man page
genesInTerm,topGOdata,missing-method Man page
getEdgeWeights Source code
getFromNode Source code
getGeneData Source code
getGraphRoot Man page Source code
getNoOfLevels Man page Source code
getPvalues Man page Source code
getSigGroups Man page
getSigGroups,topGOdata,classicCount-method Man page
getSigGroups,topGOdata,classicExpr-method Man page
getSigGroups,topGOdata,classicScore-method Man page
getSigGroups,topGOdata,elimCount-method Man page
getSigGroups,topGOdata,elimExpr-method Man page
getSigGroups,topGOdata,elimScore-method Man page
getSigGroups,topGOdata,leaCount-method Man page
getSigGroups,topGOdata,leaExpr-method Man page
getSigGroups,topGOdata,leaScore-method Man page
getSigGroups,topGOdata,pC-method Man page
getSigGroups,topGOdata,parentChild-method Man page
getSigGroups,topGOdata,weight01Count-method Man page
getSigGroups,topGOdata,weight01Expr-method Man page
getSigGroups,topGOdata,weight01Score-method Man page
getSigGroups,topGOdata,weightCount-method Man page
getSigGroups-methods Man page
getSigRatio Man page
getSigRatio,weightCount-method Man page
getTermsDefinition Source code
graph Man page
graph,topGOdata-method Man page
graph<- Man page
graph<-,topGOdata-method Man page
groupGOTerms Man page Source code
groupStats-class Man page
inducedGraph Man page Source code
initialize,classicCount-method Man page
initialize,classicExpr-method Man page
initialize,classicScore-method Man page
initialize,elimCount-method Man page
initialize,elimExpr-method Man page
initialize,elimScore-method Man page
initialize,groupStats-method Man page
initialize,leaCount-method Man page
initialize,leaExpr-method Man page
initialize,leaScore-method Man page
initialize,pC-method Man page
initialize,parentChild-method Man page
initialize,topGOdata-method Man page
initialize,topGOresult-method Man page
initialize,weight01Count-method Man page
initialize,weight01Expr-method Man page
initialize,weight01Score-method Man page
initialize,weightCount-method Man page
inverseList Man page Source code
joinFun Man page
joinFun,parentChild-method Man page
leaCount-class Man page
leaExpr-class Man page
leaScore-class Man page
mapGenes2GOgraph Source code
members Man page
members,elimScore-method Man page
members,groupStats,missing-method Man page
members,weight01Expr,missing-method Man page
members,weight01Score,missing-method Man page
members,weightCount-method Man page
members<- Man page
members<-,groupStats-method Man page
membersExpr Man page
membersExpr,classicExpr-method Man page
membersScore Man page
membersScore,classicScore-method Man page
membersScore,elimScore-method Man page
membersScore,weight01Score-method Man page
nodesInInducedGraph Man page Source code
nodesInInducedGraph2 Source code
numAllMembers Man page
numAllMembers,elimCount-method Man page
numAllMembers,elimScore-method Man page
numAllMembers,groupStats-method Man page
numAllMembers,parentChild-method Man page
numAllMembers,weight01Count-method Man page
numAllMembers,weight01Expr-method Man page
numAllMembers,weight01Score-method Man page
numAllMembers,weightCount-method Man page
numGenes Man page
numGenes,topGOdata-method Man page
numMembers Man page
numMembers,elimCount-method Man page
numMembers,elimScore-method Man page
numMembers,groupStats-method Man page
numMembers,weight01Count-method Man page
numMembers,weight01Expr-method Man page
numMembers,weight01Score-method Man page
numMembers,weightCount-method Man page
numSigAll Man page
numSigAll,classicCount-method Man page
numSigAll,elimCount-method Man page
numSigAll,parentChild-method Man page
numSigAll,weight01Count-method Man page
numSigAll,weightCount-method Man page
numSigGenes Man page
numSigGenes,topGOdata-method Man page
numSigMembers Man page
numSigMembers,classicCount-method Man page
numSigMembers,elimCount-method Man page
numSigMembers,weight01Count-method Man page
numSigMembers,weightCount-method Man page
onAttach Source code
ontology Man page
ontology,topGOdata-method Man page
ontology<- Man page
ontology<-,topGOdata-method Man page
pC-class Man page
pType Man page
pType,classicExpr-method Man page
pType<- Man page
pType<-,classicExpr-method Man page
parentChild-class Man page
penalise Man page
penalise,weightCount,numeric,numeric-method Man page
permSumStats Man page Source code
permSumStats.all Man page Source code
phenotype Man page
phenotype,topGOdata-method Man page
print,topGOdata-method Man page
print,topGOresult-method Man page
printDOT Source code
printGeneData Source code
printGenes Man page
printGenes,topGOdata,character,character-method Man page
printGenes,topGOdata,character,missing-method Man page
printGenes-methods Man page
printGraph Man page
printGraph,topGOdata,topGOresult,numeric,missing-method Man page
printGraph,topGOdata,topGOresult,numeric,topGOresult-method Man page
printGraph-methods Man page
printTopGOdata Source code
printTopGOresult Source code
ps2eps Source code
rankMembers Man page
rankMembers,classicScore-method Man page
rankMembers,elimScore-method Man page
rankMembers,weight01Score-method Man page
readMappings Man page Source code
resultFisher Man page
resultKS Man page
reverseArch Man page Source code
roundFun Man page
roundFun,weightCount-method Man page
runTest Man page
runTest,groupStats,missing,missing-method Man page
runTest,groupStats-method Man page
runTest,topGOdata,character,character-method Man page
runTest,topGOdata,missing,character-method Man page
score Man page
score,topGOresult-method Man page
score<- Man page
score<-,classicScore-method Man page
score<-,elimScore-method Man page
score<-,topGOresult-method Man page
scoreOrder Man page
scoreOrder,classicScore-method Man page
scoresInTerm Man page
scoresInTerm,topGOdata,character-method Man page
scoresInTerm,topGOdata,missing-method Man page
show,topGOdata-method Man page
show,topGOresult-method Man page
showGroupDensity Man page Source code
showSigOfNodes Man page Source code
sigAllMembers Man page
sigAllMembers,classicCount-method Man page
sigAllMembers,elimCount-method Man page
sigAllMembers,parentChild-method Man page
sigAllMembers,weight01Count-method Man page
sigAllMethods Source code
sigGenes Man page
sigGenes,topGOdata-method Man page
sigGroups.LEA Source code
sigGroups.classic Source code
sigGroups.elim Source code
sigGroups.parentChild Source code
sigGroups.weight Source code
sigGroups.weight01 Source code
sigMembers Man page
sigMembers,classicCount-method Man page
sigMembers,elimCount-method Man page
sigMembers,weight01Count-method Man page
sigMembers<- Man page
sigMembers<-,classicCount-method Man page
sigMembers<-,elimCount-method Man page
sigMembers<-,pC-method Man page
sigMembers<-,parentChild-method Man page
sigRatio Man page
sigRatio,weightCount-method Man page
sigRatio.01 Source code
sigRatio.log Source code
sigRatio.ratio Source code
sigRatio<- Man page
sigRatio<-,weightCount-method Man page
significant Man page
significant,weightCount-method Man page
termStat Man page
termStat,topGOdata,character-method Man page
termStat,topGOdata,missing-method Man page
testName Man page
testName,topGOresult-method Man page
testName<- Man page
testName<-,topGOresult-method Man page
testStatPar Man page
testStatPar,groupStats-method Man page
testStatPar,weightCount-method Man page
testStatistic Man page
testStatistic,groupStats-method Man page
testStatistic,weightCount-method Man page
topDiffGenes Man page
topGO Man page
topGO-package Man page
topGOdata-class Man page
topGOresult-class Man page
updateGenes Man page
updateGenes,topGOdata,factor,missing-method Man page
updateGenes,topGOdata,numeric,function-method Man page
updateGroup Man page
updateGroup,groupStats,character,character-method Man page
updateGroup,pC,missing,character-method Man page
updateGroup,pC,missing,missing-method Man page
updateGroup,parentChild,missing,character-method Man page
updateGroup,weightCount,character,character-method Man page
updateTerm<- Man page
updateTerm<-,topGOdata,character-method Man page
usedGO Man page
usedGO,topGOdata-method Man page
weight01Count-class Man page
weight01Expr-class Man page
weight01Score-class Man page
weightCount-class Man page
whichAlgorithms Man page Source code
whichTests Man page Source code
writeToNodes Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/topGOalgo.R
R/topGOannotations.R
R/topGOfunctions.R
R/topGOgraph.R
R/topGOmethods.R
R/topGOtests.R
R/topGOviz.R
R/zzz.R
build
build/vignette.rds
data
data/GOdata.rda
data/geneList.rda
data/results.tGO.rda
inst
inst/doc
inst/doc/topGO.R
inst/doc/topGO.Rnw
inst/doc/topGO.pdf
inst/examples
inst/examples/geneid2go.map
inst/scripts
inst/scripts/GO_ALL.R
inst/scripts/geneToGOscript.R
man
man/GOTests.Rd
man/GOdata.Rd
man/annFUN.Rd
man/classicCount-class.Rd
man/classicExpr-class.Rd
man/classicScore-class.Rd
man/dagFunctions.Rd
man/diagnosticMethods.Rd
man/elimCount-class.Rd
man/elimExpr-class.Rd
man/elimScore-class.Rd
man/geneList.Rd
man/getPvalues.Rd
man/getSigGroups.Rd
man/groupGOTerms.Rd
man/groupStats-class.Rd
man/inducedGraph.Rd
man/parentChild-class.Rd
man/printGraph-methods.Rd
man/topGO-package.Rd
man/topGOdata-class.Rd
man/topGOresult-class.Rd
man/weightCount-class.Rd
vignettes
vignettes/green_ckmark.png
vignettes/red_ckmark.png
vignettes/ref_books.bib
vignettes/topGO.Rnw
vignettes/topGO_classes_v3.pdf
topGO documentation built on May 20, 2017, 10:17 p.m.