topGO: Enrichment analysis for Gene Ontology


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Documentation for package ‘topGO’ version 1.4.0

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A B C D E F G I M N O P R S T U W

-- --

topGO-package Enrichment analysis for Gene Ontology

-- A --

allGenes Class "topGOdata"
allGenes,topGOdata-method Class "topGOdata"
allMembers Class "groupStats"
allMembers,elimScore-method Class "elimScore"
allMembers,groupStats-method Class "groupStats"
allMembers,weightCount-method Class "weightCount"
allMembers<-,groupStats-method Class "groupStats"
allScore Class "classicScore"
allScore,classicScore,logical-method Class "classicScore"
allScore,classicScore,missing-method Class "classicScore"
allScore,elimScore,logical-method Class "elimScore"
allScore,elimScore,missing-method Class "elimScore"
alternative,elimScore-method Class "elimScore"
annFUN.gene2GO functions to map gene IDs to GO terms
annFUN.GO2genes functions to map gene IDs to GO terms
annFUN.hgu functions to map gene IDs to GO terms
attrInTerm Class "topGOdata"
attrInTerm,topGOdata,character,character-method Class "topGOdata"
attrInTerm,topGOdata,character,missing-method Class "topGOdata"

-- B --

buildGOgraph.topology buils GO graph starting from the most specific GO terms
buildLevels Determines the levels of a Directed Acyclic Graph (DAG)

-- C --

classicCount-class Class "classicCount"
classicScore-class Class "classicScore"
contTable Class "classicCount"
contTable,classicCount-method Class "classicCount"
contTable,elimCount-method Class "elimCount"
countGenesInTerm Class "topGOdata"
countGenesInTerm,topGOdata,character-method Class "topGOdata"
countGenesInTerm,topGOdata,missing-method Class "topGOdata"
cutOff Class "elimCount"
cutOff,elimCount-method Class "elimCount"
cutOff,elimScore-method Class "elimScore"
cutOff<-,elimCount-method Class "elimCount"
cutOff<-,elimScore-method Class "elimScore"

-- D --

description Class "topGOdata"
description,topGOdata-method Class "topGOdata"
description,topGOresult-method Class "topGOresult"
description<-,topGOdata,ANY-method Class "topGOdata"
description<-,topGOresult,ANY-method Class "topGOresult"

-- E --

elim Class "elimCount"
elim,elimCount-method Class "elimCount"
elim,elimScore-method Class "elimScore"
elim<-,elimCount-method Class "elimCount"
elim<-,elimScore-method Class "elimScore"
elimCount-class Class "elimCount"
elimScore-class Class "elimScore"
expressionMatrix Class "topGOdata"
expressionMatrix,topGOdata-method Class "topGOdata"

-- F --

feasible Class "topGOdata"
feasible,topGOdata-method Class "topGOdata"
feasible<-,topGOdata-method Class "topGOdata"

-- G --

genes Class "topGOdata"
genes,topGOdata-method Class "topGOdata"
geneScore Class "topGOdata"
geneScore,topGOdata,character-method Class "topGOdata"
geneScore,topGOdata,missing-method Class "topGOdata"
geneScore,topGOdata-method Class "topGOdata"
geneSelectionFun Class "topGOdata"
geneSelectionFun,topGOdata-method Class "topGOdata"
geneSelectionFun<-,topGOdata-method Class "topGOdata"
genesInTerm Class "topGOdata"
genesInTerm,topGOdata,character-method Class "topGOdata"
genesInTerm,topGOdata,missing-method Class "topGOdata"
GenTable Class "topGOdata"
genTable Class "topGOdata"
genTable,topGOdata,list-method Class "topGOdata"
GenTable,topGOdata-method Class "topGOdata"
getGraphRoot Determines the levels of a Directed Acyclic Graph (DAG)
getNoOfLevels Determines the levels of a Directed Acyclic Graph (DAG)
getPvalues Function to compute p-values of a t-test for a gene expression matrix.
getSigGroups Algorithms for scoring GO terms
getSigGroups,topGOdata,classicCount-method Algorithms for scoring GO terms
getSigGroups,topGOdata,classicScore-method Algorithms for scoring GO terms
getSigGroups,topGOdata,elimCount-method Algorithms for scoring GO terms
getSigGroups,topGOdata,elimScore-method Algorithms for scoring GO terms
getSigGroups,topGOdata,weightCount-method Algorithms for scoring GO terms
getSigGroups-methods Algorithms for scoring GO terms
getSigRatio Class "weightCount"
getSigRatio,weightCount-method Class "weightCount"
GOBPTerm ~~function to do ... ~~
GOCCTerm ~~function to do ... ~~
GOdata Example of a topGO data object
GOFisherTest Fischer's exact test for gene set
GOFisherTest,classicCount-method Class "classicCount"
GOFisherTest,elimCount-method Class "elimCount"
GOKSTest Kolmogorov-Smirnov test for gene sets
GOKSTest,classicScore-method Class "classicScore"
GOKSTest,elimScore-method Class "elimScore"
GOMFTerm ~~function to do ... ~~
GOplot ~~ Methods for Function printGraph in Package ‘topGO’ ~~
GOtTest Kolmogorov-Smirnov test for gene sets
GOtTest,classicScore-method Class "classicScore"
graph Class "topGOdata"
graph,topGOdata-method Class "topGOdata"
graph<-,topGOdata-method Class "topGOdata"
groupGOTerms ~~function to do ... ~~
groupStats-class Class "groupStats"

-- I --

inducedGraph ~~function to do ... ~~
initialize,classicCount-method Class "classicCount"
initialize,classicScore-method Class "classicScore"
initialize,elimCount-method Class "elimCount"
initialize,elimScore-method Class "elimScore"
initialize,groupStats-method Class "groupStats"
initialize,topGOdata-method Class "topGOdata"
initialize,topGOresult-method Class "topGOresult"
initialize,weightCount-method Class "weightCount"

-- M --

mapGenes2GOgraph ~~function to do ... ~~
members Class "groupStats"
members,elimScore-method Class "elimScore"
members,groupStats-method Class "groupStats"
members,weightCount-method Class "weightCount"
members<-,groupStats-method Class "groupStats"
membersScore Class "classicScore"
membersScore,classicScore-method Class "classicScore"
membersScore,elimScore-method Class "elimScore"

-- N --

Name Class "groupStats"
Name,groupStats-method Class "groupStats"
Name,weightCount-method Class "weightCount"
Name<-,groupStats-method Class "groupStats"
numAllMembers Class "groupStats"
numAllMembers,elimCount-method Class "elimCount"
numAllMembers,elimScore-method Class "elimScore"
numAllMembers,groupStats-method Class "groupStats"
numAllMembers,weightCount-method Class "weightCount"
numGenes Class "topGOdata"
numGenes,topGOdata-method Class "topGOdata"
numMembers Class "groupStats"
numMembers,elimCount-method Class "elimCount"
numMembers,elimScore-method Class "elimScore"
numMembers,groupStats-method Class "groupStats"
numMembers,weightCount-method Class "weightCount"
numSigAll Class "classicCount"
numSigAll,classicCount-method Class "classicCount"
numSigAll,elimCount-method Class "elimCount"
numSigAll,weightCount-method Class "weightCount"
numSigGenes Class "topGOdata"
numSigGenes,topGOdata-method Class "topGOdata"
numSigMembers Class "classicCount"
numSigMembers,classicCount-method Class "classicCount"
numSigMembers,elimCount-method Class "elimCount"
numSigMembers,weightCount-method Class "weightCount"

-- O --

ontology Class "topGOdata"
ontology,topGOdata-method Class "topGOdata"
ontology<-,topGOdata-method Class "topGOdata"

-- P --

penalise Class "weightCount"
penalise,weightCount,numeric,numeric-method Class "weightCount"
phenotype Class "topGOdata"
phenotype,topGOdata-method Class "topGOdata"
print,topGOdata-method Class "topGOdata"
printGenes Summary for genes annotated to a GO term
printGenes,topGOdata,character,character-method Summary for genes annotated to a GO term
printGenes,topGOdata,character,missing-method Summary for genes annotated to a GO term
printGenes-methods Summary for genes annotated to a GO term
printGraph ~~ Methods for Function printGraph in Package ‘topGO’ ~~
printGraph,topGOdata,topGOresult,numeric,missing-method ~~ Methods for Function printGraph in Package ‘topGO’ ~~
printGraph,topGOdata,topGOresult,numeric,topGOresult-method ~~ Methods for Function printGraph in Package ‘topGO’ ~~
printGraph-methods ~~ Methods for Function printGraph in Package ‘topGO’ ~~

-- R --

rankMembers Class "classicScore"
rankMembers,classicScore-method Class "classicScore"
rankMembers,elimScore-method Class "elimScore"
reverseArch ~~function to do ... ~~
roundFun Class "weightCount"
roundFun,weightCount-method Class "weightCount"
run Algorithms for scoring GO terms
run,topGOdata,character,character-method Algorithms for scoring GO terms
runTest Class "groupStats"
runTest,groupStats-method Class "groupStats"

-- S --

score Class "topGOresult"
score,topGOresult-method Class "topGOresult"
score<-,classicScore-method Class "classicScore"
score<-,elimScore-method Class "elimScore"
score<-,topGOresult-method Class "topGOresult"
scoreOrder Class "classicScore"
scoreOrder,classicScore-method Class "classicScore"
scoresInTerm Class "topGOdata"
scoresInTerm,topGOdata,character-method Class "topGOdata"
scoresInTerm,topGOdata,missing-method Class "topGOdata"
show,topGOdata-method Class "topGOdata"
showSigOfNodes ~~ Methods for Function printGraph in Package ‘topGO’ ~~
sigAllMembers Class "classicCount"
sigAllMembers,classicCount-method Class "classicCount"
sigAllMembers,elimCount-method Class "elimCount"
sigGenes Class "topGOdata"
sigGenes,topGOdata-method Class "topGOdata"
sigMembers Class "classicCount"
sigMembers,classicCount-method Class "classicCount"
sigMembers,elimCount-method Class "elimCount"
sigMembers<-,classicCount-method Class "classicCount"
sigMembers<-,elimCount-method Class "elimCount"
significant Class "weightCount"
significant,weightCount-method Class "weightCount"
sigRatio Class "weightCount"
sigRatio,weightCount-method Class "weightCount"
sigRatio<-,weightCount-method Class "weightCount"

-- T --

termStat Class "topGOdata"
termStat,topGOdata,character-method Class "topGOdata"
termStat,topGOdata,missing-method Class "topGOdata"
testClass Class "topGOresult"
testClass,topGOresult-method Class "topGOresult"
testClass<-,topGOresult-method Class "topGOresult"
testName Class "topGOresult"
testName,topGOresult-method Class "topGOresult"
testName<-,topGOresult-method Class "topGOresult"
testStatistic Class "groupStats"
testStatistic,groupStats-method Class "groupStats"
testStatistic,weightCount-method Class "weightCount"
testStatPar Class "groupStats"
testStatPar,groupStats-method Class "groupStats"
testStatPar,weightCount-method Class "weightCount"
topGO Enrichment analysis for Gene Ontology
topGOdata-class Class "topGOdata"
topGOresult-class Class "topGOresult"

-- U --

updateGenes Class "topGOdata"
updateGenes,topGOdata,factor,missing-method Class "topGOdata"
updateGenes,topGOdata,numeric,function-method Class "topGOdata"
updateGroup Class "groupStats"
updateGroup,groupStats,character,character-method Class "groupStats"
updateGroup,weightCount,character,character-method Class "weightCount"
updateTerm<-,topGOdata,character-method Class "topGOdata"
usedGO Class "topGOdata"
usedGO,topGOdata-method Class "topGOdata"

-- W --

weightCount-class Class "weightCount"
Weights Class "weightCount"
Weights,weightCount,logical-method Class "weightCount"
Weights,weightCount,missing-method Class "weightCount"
Weights,weightCount-method Class "weightCount"
Weights<-,weightCount-method Class "weightCount"
weightScore-class Class "weightScore" ~~~