Enrichment Analysis for Gene Ontology


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Documentation for package ‘topGO’ version 2.50.0

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topGO-package Enrichment analysis for Gene Ontology

-- A --

affyLib A toy example of a list of gene identifiers and the respective p-values
algorithm Class "topGOresult"
algorithm-method Class "topGOresult"
algorithm<- Class "topGOresult"
algorithm<--method Class "topGOresult"
allGenes Class "topGOdata"
allGenes-method Class "topGOdata"
allMembers Class "groupStats"
allMembers-method Class "elimExpr"
allMembers-method Classes "elimScore" and "weight01Score"
allMembers-method Class "groupStats"
allMembers-method Classes "parentChild" and "pC"
allMembers-method Class "weightCount"
allMembers<- Class "groupStats"
allMembers<--method Class "classicExpr"
allMembers<--method Class "groupStats"
allMembers<--method Classes "parentChild" and "pC"
allParents Classes "parentChild" and "pC"
allParents-method Classes "parentChild" and "pC"
allScore Class "classicScore"
allScore-method Class "classicScore"
allScore-method Classes "elimScore" and "weight01Score"
alternative-method Classes "elimScore" and "weight01Score"
annFUN Functions which map gene identifiers to GO terms
annFUN.db Functions which map gene identifiers to GO terms
annFUN.file Functions which map gene identifiers to GO terms
annFUN.gene2GO Functions which map gene identifiers to GO terms
annFUN.GO2genes Functions which map gene identifiers to GO terms
annFUN.org Functions which map gene identifiers to GO terms
attrInTerm Class "topGOdata"
attrInTerm-method Class "topGOdata"

-- B --

buildLevels Utility functions to work with Directed Acyclic Graphs (DAG)

-- C --

classicCount-class Class "classicCount"
classicExpr-class Class "classicExpr"
classicScore-class Class "classicScore"
combineResults Class "topGOresult"
contTable Class "classicCount"
contTable-method Class "classicCount"
contTable-method Classes "elimCount" and "weight01Count"
countGenesInTerm Class "topGOdata"
countGenesInTerm-method Class "topGOdata"
cutOff Classes "elimCount" and "weight01Count"
cutOff-method Classes "elimCount" and "weight01Count"
cutOff-method Class "elimExpr"
cutOff-method Classes "elimScore" and "weight01Score"
cutOff<- Classes "elimCount" and "weight01Count"
cutOff<--method Classes "elimCount" and "weight01Count"
cutOff<--method Class "elimExpr"
cutOff<--method Classes "elimScore" and "weight01Score"

-- D --

depth Classes "elimCount" and "weight01Count"
depth-method Classes "elimCount" and "weight01Count"
depth-method Class "elimExpr"
depth-method Classes "elimScore" and "weight01Score"
depth<- Classes "elimCount" and "weight01Count"
depth<--method Classes "elimCount" and "weight01Count"
depth<--method Class "elimExpr"
depth<--method Classes "elimScore" and "weight01Score"
description Class "topGOdata"
description-method Class "topGOdata"
description-method Class "topGOresult"
description<- Class "topGOdata"
description<--method Class "topGOdata"
description<--method Class "topGOresult"

-- E --

elim Classes "elimCount" and "weight01Count"
elim-method Classes "elimCount" and "weight01Count"
elim-method Class "elimExpr"
elim-method Classes "elimScore" and "weight01Score"
elim<- Classes "elimCount" and "weight01Count"
elim<--method Classes "elimCount" and "weight01Count"
elim<--method Class "elimExpr"
elim<--method Classes "elimScore" and "weight01Score"
elimCount-class Classes "elimCount" and "weight01Count"
elimExpr-class Class "elimExpr"
elimScore-class Classes "elimScore" and "weight01Score"
emptyExpr-method Class "classicExpr"
expressionMatrix Class "topGOdata"
expressionMatrix-method Class "topGOdata"

-- F --

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

-- G --

geneData Class "topGOresult"
geneData-method Class "topGOresult"
geneData<- Class "topGOresult"
geneData<--method Class "topGOresult"
geneList A toy example of a list of gene identifiers and the respective p-values
genes Class "topGOdata"
genes-method Class "topGOdata"
geneScore Class "topGOdata"
geneScore-method Class "topGOdata"
geneSelectionFun Class "topGOdata"
geneSelectionFun-method Class "topGOdata"
geneSelectionFun<- Class "topGOdata"
geneSelectionFun<--method Class "topGOdata"
genesInTerm Class "topGOdata"
genesInTerm-method Class "topGOdata"
GenTable Diagnostic functions for topGOdata and topGOresult objects.
GenTable-method Diagnostic functions for topGOdata and topGOresult objects.
getGraphRoot Utility functions to work with Directed Acyclic Graphs (DAG)
getNoOfLevels Utility functions to work with Directed Acyclic Graphs (DAG)
getPvalues Convenient function to compute p-values from a gene expression matrix.
getSigGroups Interfaces for running the enrichment tests
getSigGroups-method Interfaces for running the enrichment tests
getSigGroups-methods Interfaces for running the enrichment tests
getSigRatio Class "weightCount"
getSigRatio-method Class "weightCount"
GOBPTerm Grouping of GO terms into the three ontologies
GOCCTerm Grouping of GO terms into the three ontologies
GOdata Sample topGOdata and topGOresult objects
GOFisherTest Gene set tests statistics
GOFisherTest-method Class "classicCount"
GOFisherTest-method Classes "elimCount" and "weight01Count"
GOglobalTest Gene set tests statistics
GOglobalTest-method Class "classicExpr"
GOKSTest Gene set tests statistics
GOKSTest-method Class "classicScore"
GOKSTiesTest Gene set tests statistics
GOKSTiesTest-method Class "classicScore"
GOMFTerm Grouping of GO terms into the three ontologies
GOplot Visualisation functions
GOSumTest Gene set tests statistics
GOSumTest-method Class "classicScore"
GOtTest Gene set tests statistics
GOtTest-method Class "classicScore"
graph Class "topGOdata"
graph-method Class "topGOdata"
graph<- Class "topGOdata"
graph<--method Class "topGOdata"
groupGOTerms Grouping of GO terms into the three ontologies
groupStats-class Class "groupStats"

-- I --

inducedGraph The subgraph induced by a set of nodes.
initialize-method Class "classicCount"
initialize-method Class "classicExpr"
initialize-method Class "classicScore"
initialize-method Classes "elimCount" and "weight01Count"
initialize-method Class "elimExpr"
initialize-method Classes "elimScore" and "weight01Score"
initialize-method Class "groupStats"
initialize-method Classes "parentChild" and "pC"
initialize-method Class "topGOdata"
initialize-method Class "topGOresult"
initialize-method Class "weightCount"
inverseList Functions which map gene identifiers to GO terms

-- J --

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

-- L --

leaCount-class Classes "elimCount" and "weight01Count"
leaExpr-class Class "elimExpr"
leaScore-class Classes "elimScore" and "weight01Score"

-- M --

members Class "groupStats"
members-method Class "elimExpr"
members-method Classes "elimScore" and "weight01Score"
members-method Class "groupStats"
members-method Class "weightCount"
members<- Class "groupStats"
members<--method Class "groupStats"
membersExpr Class "classicExpr"
membersExpr-method Class "classicExpr"
membersScore Class "classicScore"
membersScore-method Class "classicScore"
membersScore-method Classes "elimScore" and "weight01Score"

-- N --

Name Class "groupStats"
Name-method Class "groupStats"
Name-method Class "weightCount"
Name<- Class "groupStats"
Name<--method Class "groupStats"
nodesInInducedGraph The subgraph induced by a set of nodes.
numAllMembers Class "groupStats"
numAllMembers-method Classes "elimCount" and "weight01Count"
numAllMembers-method Class "elimExpr"
numAllMembers-method Classes "elimScore" and "weight01Score"
numAllMembers-method Class "groupStats"
numAllMembers-method Classes "parentChild" and "pC"
numAllMembers-method Class "weightCount"
numGenes Class "topGOdata"
numGenes-method Class "topGOdata"
numMembers Class "groupStats"
numMembers-method Classes "elimCount" and "weight01Count"
numMembers-method Class "elimExpr"
numMembers-method Classes "elimScore" and "weight01Score"
numMembers-method Class "groupStats"
numMembers-method Class "weightCount"
numSigAll Class "classicCount"
numSigAll-method Class "classicCount"
numSigAll-method Classes "elimCount" and "weight01Count"
numSigAll-method Classes "parentChild" and "pC"
numSigAll-method Class "weightCount"
numSigGenes Class "topGOdata"
numSigGenes-method Class "topGOdata"
numSigMembers Class "classicCount"
numSigMembers-method Class "classicCount"
numSigMembers-method Classes "elimCount" and "weight01Count"
numSigMembers-method Class "weightCount"

-- O --

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

-- P --

parentChild-class Classes "parentChild" and "pC"
pC-class Classes "parentChild" and "pC"
penalise Class "weightCount"
penalise-method Class "weightCount"
permSumStats Gene set tests statistics
permSumStats.all Gene set tests statistics
phenotype Class "topGOdata"
phenotype-method Class "topGOdata"
print-method Class "topGOdata"
print-method Class "topGOresult"
printGenes Diagnostic functions for topGOdata and topGOresult objects.
printGenes-method Diagnostic functions for topGOdata and topGOresult objects.
printGenes-methods Diagnostic functions for topGOdata and topGOresult objects.
printGraph Visualisation functions
printGraph-method Visualisation functions
printGraph-methods Visualisation functions
pType Class "classicExpr"
pType-method Class "classicExpr"
pType<- Class "classicExpr"
pType<--method Class "classicExpr"

-- R --

rankMembers Class "classicScore"
rankMembers-method Class "classicScore"
rankMembers-method Classes "elimScore" and "weight01Score"
readMappings Functions which map gene identifiers to GO terms
resultFisher Sample topGOdata and topGOresult objects
resultKS Sample topGOdata and topGOresult objects
reverseArch Utility functions to work with Directed Acyclic Graphs (DAG)
roundFun Class "weightCount"
roundFun-method Class "weightCount"
runTest Interfaces for running the enrichment tests
runTest-method Interfaces for running the enrichment tests
runTest-method Class "groupStats"

-- S --

score Class "topGOresult"
score-method Class "topGOresult"
score<- Class "classicScore"
score<--method Class "classicScore"
score<--method Classes "elimScore" and "weight01Score"
score<--method Class "topGOresult"
scoreOrder Class "classicScore"
scoreOrder-method Class "classicScore"
scoresInTerm Class "topGOdata"
scoresInTerm-method Class "topGOdata"
show-method Class "topGOdata"
show-method Class "topGOresult"
showGroupDensity Diagnostic functions for topGOdata and topGOresult objects.
showSigOfNodes Visualisation functions
sigAllMembers Class "classicCount"
sigAllMembers-method Class "classicCount"
sigAllMembers-method Classes "elimCount" and "weight01Count"
sigAllMembers-method Classes "parentChild" and "pC"
sigGenes Class "topGOdata"
sigGenes-method Class "topGOdata"
sigMembers Class "classicCount"
sigMembers-method Class "classicCount"
sigMembers-method Classes "elimCount" and "weight01Count"
sigMembers<- Class "classicCount"
sigMembers<--method Class "classicCount"
sigMembers<--method Classes "elimCount" and "weight01Count"
sigMembers<--method Classes "parentChild" and "pC"
significant Class "weightCount"
significant-method Class "weightCount"
sigRatio Class "weightCount"
sigRatio-method Class "weightCount"
sigRatio<- Class "weightCount"
sigRatio<--method Class "weightCount"

-- T --

termStat Class "topGOdata"
termStat-method Class "topGOdata"
testName Class "topGOresult"
testName-method Class "topGOresult"
testName<- Class "topGOresult"
testName<--method Class "topGOresult"
testStatistic Class "groupStats"
testStatistic-method Class "groupStats"
testStatistic-method Class "weightCount"
testStatPar Class "groupStats"
testStatPar-method Class "groupStats"
testStatPar-method Class "weightCount"
topDiffGenes A toy example of a list of gene identifiers and the respective p-values
topGO Enrichment analysis for Gene Ontology
topGOdata-class Class "topGOdata"
topGOresult-class Class "topGOresult"

-- U --

updateGenes Class "topGOdata"
updateGenes-method Class "topGOdata"
updateGroup Class "groupStats"
updateGroup-method Class "groupStats"
updateGroup-method Classes "parentChild" and "pC"
updateGroup-method Class "weightCount"
updateTerm<- Class "topGOdata"
updateTerm<--method Class "topGOdata"
usedGO Class "topGOdata"
usedGO-method Class "topGOdata"

-- W --

weight01Count-class Classes "elimCount" and "weight01Count"
weight01Expr-class Class "elimExpr"
weight01Score-class Classes "elimScore" and "weight01Score"
weightCount-class Class "weightCount"
Weights Class "weightCount"
Weights-method Class "weightCount"
Weights<- Class "weightCount"
Weights<--method Class "weightCount"
whichAlgorithms Interfaces for running the enrichment tests
whichTests Interfaces for running the enrichment tests