| 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" |