A B C D E F G I J L M N O P R S T U W
topGO-package | Enrichment analysis for Gene Ontology |
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" |
buildLevels | Utility functions to work with Directed Acyclic Graphs (DAG) |
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" |
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" |
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" |
feasible | Class "topGOdata" |
feasible-method | Class "topGOdata" |
feasible<- | Class "topGOdata" |
feasible<--method | Class "topGOdata" |
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" |
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 |
joinFun | Classes "parentChild" and "pC" |
joinFun-method | Classes "parentChild" and "pC" |
leaCount-class | Classes "elimCount" and "weight01Count" |
leaExpr-class | Class "elimExpr" |
leaScore-class | Classes "elimScore" and "weight01Score" |
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" |
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" |
ontology | Class "topGOdata" |
ontology-method | Class "topGOdata" |
ontology<- | Class "topGOdata" |
ontology<--method | Class "topGOdata" |
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" |
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" |
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" |
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" |
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" |
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 |