topGO: Enrichment analysis for Gene Ontology


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Documentation for package ‘topGO’ version 1.8.1

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A B C D E F G I J 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 Classes "elimScore" and "removeScore"
allMembers,groupStats-method Class "groupStats"
allMembers,parentChild-method Classes "parentChild" and "pC"
allMembers,removeExpr-method Class "elimExpr" ~~~
allMembers,removeScore-method Classes "elimScore" and "removeScore"
allMembers,weightCount-method Class "weightCount"
allMembers<-,classicExpr-method Class "classicExpr" ~~~
allMembers<-,groupStats-method Class "groupStats"
allMembers<-,parentChild-method Classes "parentChild" and "pC"
allMembers<-,pC-method Classes "parentChild" and "pC"
allParents Classes "parentChild" and "pC"
allParents,parentChild-method Classes "parentChild" and "pC"
allScore Class "classicScore"
allScore,classicScore,logical-method Class "classicScore"
allScore,classicScore,missing-method Class "classicScore"
allScore,elimScore,logical-method Classes "elimScore" and "removeScore"
allScore,elimScore,missing-method Classes "elimScore" and "removeScore"
allScore,removeScore,logical-method Classes "elimScore" and "removeScore"
allScore,removeScore,missing-method Classes "elimScore" and "removeScore"
alternative,elimScore-method Classes "elimScore" and "removeScore"
annFUN 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"
classicExpr-class Class "classicExpr" ~~~
classicScore-class Class "classicScore"
contTable Class "classicCount"
contTable,classicCount-method Class "classicCount"
contTable,elimCount-method Classes "elimCount" and "removeCount"
countGenesInTerm Class "topGOdata"
countGenesInTerm,topGOdata,character-method Class "topGOdata"
countGenesInTerm,topGOdata,missing-method Class "topGOdata"
cutOff Classes "elimCount" and "removeCount"
cutOff,elimCount-method Classes "elimCount" and "removeCount"
cutOff,elimExpr-method Class "elimExpr" ~~~
cutOff,elimScore-method Classes "elimScore" and "removeScore"
cutOff<-,elimCount-method Classes "elimCount" and "removeCount"
cutOff<-,elimExpr-method Class "elimExpr" ~~~
cutOff<-,elimScore-method Classes "elimScore" and "removeScore"

-- 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 Classes "elimCount" and "removeCount"
elim,elimCount-method Classes "elimCount" and "removeCount"
elim,elimScore-method Classes "elimScore" and "removeScore"
elim,removeCount-method Classes "elimCount" and "removeCount"
elim,removeExpr-method Class "elimExpr" ~~~
elim,removeScore-method Classes "elimScore" and "removeScore"
elim<-,elimCount-method Classes "elimCount" and "removeCount"
elim<-,elimScore-method Classes "elimScore" and "removeScore"
elim<-,removeCount-method Classes "elimCount" and "removeCount"
elim<-,removeExpr-method Class "elimExpr" ~~~
elim<-,removeScore-method Classes "elimScore" and "removeScore"
elimCount-class Classes "elimCount" and "removeCount"
elimExpr-class Class "elimExpr" ~~~
elimScore-class Classes "elimScore" and "removeScore"
emptyExpr,classicExpr-method Class "classicExpr" ~~~
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,classicExpr-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,elimExpr-method Algorithms for scoring GO terms
getSigGroups,topGOdata,elimScore-method Algorithms for scoring GO terms
getSigGroups,topGOdata,parentChild-method Algorithms for scoring GO terms
getSigGroups,topGOdata,pC-method Algorithms for scoring GO terms
getSigGroups,topGOdata,removeCount-method Algorithms for scoring GO terms
getSigGroups,topGOdata,removeExpr-method Algorithms for scoring GO terms
getSigGroups,topGOdata,removeScore-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 Classes "elimCount" and "removeCount"
GOglobalTest Globaltest for gene sets
GOglobalTest,classicExpr-method Class "classicExpr" ~~~
GOKSTest Kolmogorov-Smirnov test for gene sets
GOKSTest,classicScore-method Class "classicScore"
GOKSTest,elimScore-method Classes "elimScore" and "removeScore"
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,classicExpr-method Class "classicExpr" ~~~
initialize,classicScore-method Class "classicScore"
initialize,elimCount-method Classes "elimCount" and "removeCount"
initialize,elimExpr-method Class "elimExpr" ~~~
initialize,elimScore-method Classes "elimScore" and "removeScore"
initialize,groupStats-method Class "groupStats"
initialize,parentChild-method Classes "parentChild" and "pC"
initialize,pC-method Classes "parentChild" and "pC"
initialize,removeCount-method Classes "elimCount" and "removeCount"
initialize,removeExpr-method Class "elimExpr" ~~~
initialize,removeScore-method Classes "elimScore" and "removeScore"
initialize,topGOdata-method Class "topGOdata"
initialize,topGOresult-method Class "topGOresult"
initialize,weightCount-method Class "weightCount"

-- J --

joinFun Classes "parentChild" and "pC"
joinFun,parentChild-method Classes "parentChild" and "pC"

-- M --

mapGenes2GOgraph ~~function to do ... ~~
members Class "groupStats"
members,elimScore-method Classes "elimScore" and "removeScore"
members,groupStats-method Class "groupStats"
members,removeExpr-method Class "elimExpr" ~~~
members,removeScore-method Classes "elimScore" and "removeScore"
members,weightCount-method Class "weightCount"
members<-,groupStats-method Class "groupStats"
membersExpr Class "classicExpr" ~~~
membersExpr,classicExpr-method Class "classicExpr" ~~~
membersScore Class "classicScore"
membersScore,classicScore-method Class "classicScore"
membersScore,elimScore-method Classes "elimScore" and "removeScore"
membersScore,removeScore-method Classes "elimScore" and "removeScore"

-- 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 Classes "elimCount" and "removeCount"
numAllMembers,elimScore-method Classes "elimScore" and "removeScore"
numAllMembers,groupStats-method Class "groupStats"
numAllMembers,parentChild-method Classes "parentChild" and "pC"
numAllMembers,removeCount-method Classes "elimCount" and "removeCount"
numAllMembers,removeExpr-method Class "elimExpr" ~~~
numAllMembers,removeScore-method Classes "elimScore" and "removeScore"
numAllMembers,weightCount-method Class "weightCount"
numGenes Class "topGOdata"
numGenes,topGOdata-method Class "topGOdata"
numMembers Class "groupStats"
numMembers,elimCount-method Classes "elimCount" and "removeCount"
numMembers,elimScore-method Classes "elimScore" and "removeScore"
numMembers,groupStats-method Class "groupStats"
numMembers,removeCount-method Classes "elimCount" and "removeCount"
numMembers,removeExpr-method Class "elimExpr" ~~~
numMembers,removeScore-method Classes "elimScore" and "removeScore"
numMembers,weightCount-method Class "weightCount"
numSigAll Class "classicCount"
numSigAll,classicCount-method Class "classicCount"
numSigAll,elimCount-method Classes "elimCount" and "removeCount"
numSigAll,parentChild-method Classes "parentChild" and "pC"
numSigAll,removeCount-method Classes "elimCount" and "removeCount"
numSigAll,weightCount-method Class "weightCount"
numSigGenes Class "topGOdata"
numSigGenes,topGOdata-method Class "topGOdata"
numSigMembers Class "classicCount"
numSigMembers,classicCount-method Class "classicCount"
numSigMembers,elimCount-method Classes "elimCount" and "removeCount"
numSigMembers,removeCount-method Classes "elimCount" and "removeCount"
numSigMembers,weightCount-method Class "weightCount"

-- O --

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

-- P --

parentChild-class Classes "parentChild" and "pC"
pC-class Classes "parentChild" and "pC"
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’ ~~
pType Class "classicExpr" ~~~
pType,classicExpr-method Class "classicExpr" ~~~
pType<-,classicExpr-method Class "classicExpr" ~~~

-- R --

rankMembers Class "classicScore"
rankMembers,classicScore-method Class "classicScore"
rankMembers,elimScore-method Classes "elimScore" and "removeScore"
rankMembers,removeScore-method Classes "elimScore" and "removeScore"
removeCount-class Classes "elimCount" and "removeCount"
removeExpr-class Class "elimExpr" ~~~
removeScore-class Classes "elimScore" and "removeScore"
reverseArch ~~function to do ... ~~
roundFun Class "weightCount"
roundFun,weightCount-method Class "weightCount"
runTest Algorithms for scoring GO terms
runTest,groupStats,missing,missing-method Class "groupStats"
runTest,groupStats-method Class "groupStats"
runTest,topGOdata,character,character-method Algorithms for scoring GO terms
runTest,topGOdata,missing,character-method Algorithms for scoring GO terms

-- S --

score Class "topGOresult"
score,topGOresult-method Class "topGOresult"
score<-,classicScore-method Class "classicScore"
score<-,elimScore-method Classes "elimScore" and "removeScore"
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 Classes "elimCount" and "removeCount"
sigAllMembers,parentChild-method Classes "parentChild" and "pC"
sigAllMembers,removeCount-method Classes "elimCount" and "removeCount"
sigGenes Class "topGOdata"
sigGenes,topGOdata-method Class "topGOdata"
sigMembers Class "classicCount"
sigMembers,classicCount-method Class "classicCount"
sigMembers,elimCount-method Classes "elimCount" and "removeCount"
sigMembers,removeCount-method Classes "elimCount" and "removeCount"
sigMembers<-,classicCount-method Class "classicCount"
sigMembers<-,elimCount-method Classes "elimCount" and "removeCount"
sigMembers<-,parentChild-method Classes "parentChild" and "pC"
sigMembers<-,pC-method Classes "parentChild" and "pC"
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,parentChild,missing,character-method Classes "parentChild" and "pC"
updateGroup,pC,missing,character-method Classes "parentChild" and "pC"
updateGroup,pC,missing,missing-method Classes "parentChild" and "pC"
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" ~~~