algorithm |
Class "topGOresult" |
algorithm,topGOresult-method |
Class "topGOresult" |
algorithm<- |
Class "topGOresult" |
algorithm<-,topGOresult-method |
Class "topGOresult" |
allGenes |
Class "topGOdata" |
allGenes,topGOdata-method |
Class "topGOdata" |
allMembers |
Class "groupStats" |
allMembers,elimScore-method |
Classes "elimScore" and "weight01Score" |
allMembers,groupStats-method |
Class "groupStats" |
allMembers,parentChild-method |
Classes "parentChild" and "pC" |
allMembers,weight01Expr-method |
Class "elimExpr" ~~~ |
allMembers,weight01Score-method |
Classes "elimScore" and "weight01Score" |
allMembers,weightCount-method |
Class "weightCount" |
allMembers<- |
Class "groupStats" |
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 "weight01Score" |
allScore,elimScore,missing-method |
Classes "elimScore" and "weight01Score" |
allScore,weight01Score,logical-method |
Classes "elimScore" and "weight01Score" |
allScore,weight01Score,missing-method |
Classes "elimScore" and "weight01Score" |
alternative,elimScore-method |
Classes "elimScore" and "weight01Score" |
annFUN |
functions to map gene IDs to GO terms |
annFUN.db |
functions to map gene IDs to GO terms |
annFUN.file |
functions to map gene IDs to GO terms |
annFUN.gene2GO |
functions to map gene IDs to GO terms |
annFUN.GO2genes |
functions to map gene IDs to GO terms |
annFUN.org |
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" |
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 "weight01Count" |
countGenesInTerm |
Class "topGOdata" |
countGenesInTerm,topGOdata,character-method |
Class "topGOdata" |
countGenesInTerm,topGOdata,missing-method |
Class "topGOdata" |
cutOff |
Classes "elimCount" and "weight01Count" |
cutOff,elimCount-method |
Classes "elimCount" and "weight01Count" |
cutOff,elimExpr-method |
Class "elimExpr" ~~~ |
cutOff,elimScore-method |
Classes "elimScore" and "weight01Score" |
cutOff<- |
Classes "elimCount" and "weight01Count" |
cutOff<-,elimCount-method |
Classes "elimCount" and "weight01Count" |
cutOff<-,elimExpr-method |
Class "elimExpr" ~~~ |
cutOff<-,elimScore-method |
Classes "elimScore" and "weight01Score" |
elim |
Classes "elimCount" and "weight01Count" |
elim,elimCount-method |
Classes "elimCount" and "weight01Count" |
elim,elimScore-method |
Classes "elimScore" and "weight01Score" |
elim,weight01Count-method |
Classes "elimCount" and "weight01Count" |
elim,weight01Expr-method |
Class "elimExpr" ~~~ |
elim,weight01Score-method |
Classes "elimScore" and "weight01Score" |
elim<- |
Classes "elimCount" and "weight01Count" |
elim<-,elimCount-method |
Classes "elimCount" and "weight01Count" |
elim<-,elimScore-method |
Classes "elimScore" and "weight01Score" |
elim<-,weight01Count-method |
Classes "elimCount" and "weight01Count" |
elim<-,weight01Expr-method |
Class "elimExpr" ~~~ |
elim<-,weight01Score-method |
Classes "elimScore" and "weight01Score" |
elimCount-class |
Classes "elimCount" and "weight01Count" |
elimExpr-class |
Class "elimExpr" ~~~ |
elimScore-class |
Classes "elimScore" and "weight01Score" |
emptyExpr,classicExpr-method |
Class "classicExpr" ~~~ |
expressionMatrix |
Class "topGOdata" |
expressionMatrix,topGOdata-method |
Class "topGOdata" |
geneData |
Class "topGOresult" |
geneData,topGOresult-method |
Class "topGOresult" |
geneData<- |
Class "topGOresult" |
geneData<-,topGOresult-method |
Class "topGOresult" |
geneList |
A toy example of a list of gene identifiers and the respective p-values |
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<- |
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 |
Utility functions for Directed Acyclic Graphs (DAG) |
getNoOfLevels |
Utility functions for Directed Acyclic Graphs (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,weight01Count-method |
Algorithms for scoring GO terms |
getSigGroups,topGOdata,weight01Expr-method |
Algorithms for scoring GO terms |
getSigGroups,topGOdata,weight01Score-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 |
Gene set tests statistics |
GOFisherTest,classicCount-method |
Class "classicCount" |
GOFisherTest,elimCount-method |
Classes "elimCount" and "weight01Count" |
GOglobalTest |
Gene set tests statistics |
GOglobalTest,classicExpr-method |
Class "classicExpr" ~~~ |
GOKSTest |
Gene set tests statistics |
GOKSTest,classicScore-method |
Class "classicScore" |
GOKSTest,elimScore-method |
Classes "elimScore" and "weight01Score" |
GOMFTerm |
~~function to do ... ~~ |
GOplot |
~~ Methods for Function printGraph in Package 'topGO' ~~ |
GOtTest |
Gene set tests statistics |
GOtTest,classicScore-method |
Class "classicScore" |
graph |
Class "topGOdata" |
graph,topGOdata-method |
Class "topGOdata" |
graph<- |
Class "topGOdata" |
graph<-,topGOdata-method |
Class "topGOdata" |
groupGOTerms |
~~function to do ... ~~ |
groupStats-class |
Class "groupStats" |
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 "weight01Count" |
initialize,elimExpr-method |
Class "elimExpr" ~~~ |
initialize,elimScore-method |
Classes "elimScore" and "weight01Score" |
initialize,groupStats-method |
Class "groupStats" |
initialize,parentChild-method |
Classes "parentChild" and "pC" |
initialize,pC-method |
Classes "parentChild" and "pC" |
initialize,topGOdata-method |
Class "topGOdata" |
initialize,topGOresult-method |
Class "topGOresult" |
initialize,weight01Count-method |
Classes "elimCount" and "weight01Count" |
initialize,weight01Expr-method |
Class "elimExpr" ~~~ |
initialize,weight01Score-method |
Classes "elimScore" and "weight01Score" |
initialize,weightCount-method |
Class "weightCount" |
inverseList |
functions to map gene IDs to GO terms |
members |
Class "groupStats" |
members,elimScore-method |
Classes "elimScore" and "weight01Score" |
members,groupStats-method |
Class "groupStats" |
members,weight01Expr-method |
Class "elimExpr" ~~~ |
members,weight01Score-method |
Classes "elimScore" and "weight01Score" |
members,weightCount-method |
Class "weightCount" |
members<- |
Class "groupStats" |
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 "weight01Score" |
membersScore,weight01Score-method |
Classes "elimScore" and "weight01Score" |
Name |
Class "groupStats" |
Name,groupStats-method |
Class "groupStats" |
Name,weightCount-method |
Class "weightCount" |
Name<- |
Class "groupStats" |
Name<-,groupStats-method |
Class "groupStats" |
nodesInInducedGraph |
~~function to do ... ~~ |
numAllMembers |
Class "groupStats" |
numAllMembers,elimCount-method |
Classes "elimCount" and "weight01Count" |
numAllMembers,elimScore-method |
Classes "elimScore" and "weight01Score" |
numAllMembers,groupStats-method |
Class "groupStats" |
numAllMembers,parentChild-method |
Classes "parentChild" and "pC" |
numAllMembers,weight01Count-method |
Classes "elimCount" and "weight01Count" |
numAllMembers,weight01Expr-method |
Class "elimExpr" ~~~ |
numAllMembers,weight01Score-method |
Classes "elimScore" and "weight01Score" |
numAllMembers,weightCount-method |
Class "weightCount" |
numGenes |
Class "topGOdata" |
numGenes,topGOdata-method |
Class "topGOdata" |
numMembers |
Class "groupStats" |
numMembers,elimCount-method |
Classes "elimCount" and "weight01Count" |
numMembers,elimScore-method |
Classes "elimScore" and "weight01Score" |
numMembers,groupStats-method |
Class "groupStats" |
numMembers,weight01Count-method |
Classes "elimCount" and "weight01Count" |
numMembers,weight01Expr-method |
Class "elimExpr" ~~~ |
numMembers,weight01Score-method |
Classes "elimScore" and "weight01Score" |
numMembers,weightCount-method |
Class "weightCount" |
numSigAll |
Class "classicCount" |
numSigAll,classicCount-method |
Class "classicCount" |
numSigAll,elimCount-method |
Classes "elimCount" and "weight01Count" |
numSigAll,parentChild-method |
Classes "parentChild" and "pC" |
numSigAll,weight01Count-method |
Classes "elimCount" and "weight01Count" |
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 "weight01Count" |
numSigMembers,weight01Count-method |
Classes "elimCount" and "weight01Count" |
numSigMembers,weightCount-method |
Class "weightCount" |
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" |
print,topGOresult-method |
Class "topGOresult" |
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<- |
Class "classicExpr" ~~~ |
pType<-,classicExpr-method |
Class "classicExpr" ~~~ |
rankMembers |
Class "classicScore" |
rankMembers,classicScore-method |
Class "classicScore" |
rankMembers,elimScore-method |
Classes "elimScore" and "weight01Score" |
rankMembers,weight01Score-method |
Classes "elimScore" and "weight01Score" |
readMappings |
functions to map gene IDs to GO terms |
reverseArch |
Utility functions for Directed Acyclic Graphs (DAG) |
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 |
score |
Class "topGOresult" |
score,topGOresult,character-method |
Class "topGOresult" |
score,topGOresult,missing-method |
Class "topGOresult" |
score<- |
Class "classicScore" |
score<-,classicScore-method |
Class "classicScore" |
score<-,elimScore-method |
Classes "elimScore" and "weight01Score" |
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" |
show,topGOresult-method |
Class "topGOresult" |
showGroupDensity |
~~ Methods for Function printGraph in Package 'topGO' ~~ |
showSigOfNodes |
~~ Methods for Function printGraph in Package 'topGO' ~~ |
sigAllMembers |
Class "classicCount" |
sigAllMembers,classicCount-method |
Class "classicCount" |
sigAllMembers,elimCount-method |
Classes "elimCount" and "weight01Count" |
sigAllMembers,parentChild-method |
Classes "parentChild" and "pC" |
sigAllMembers,weight01Count-method |
Classes "elimCount" and "weight01Count" |
sigGenes |
Class "topGOdata" |
sigGenes,topGOdata-method |
Class "topGOdata" |
sigMembers |
Class "classicCount" |
sigMembers,classicCount-method |
Class "classicCount" |
sigMembers,elimCount-method |
Classes "elimCount" and "weight01Count" |
sigMembers,weight01Count-method |
Classes "elimCount" and "weight01Count" |
sigMembers<- |
Class "classicCount" |
sigMembers<-,classicCount-method |
Class "classicCount" |
sigMembers<-,elimCount-method |
Classes "elimCount" and "weight01Count" |
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<- |
Class "weightCount" |
sigRatio<-,weightCount-method |
Class "weightCount" |
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<- |
Class "topGOdata" |
updateTerm<-,topGOdata,character-method |
Class "topGOdata" |
usedGO |
Class "topGOdata" |
usedGO,topGOdata-method |
Class "topGOdata" |