| .countsInNode |
Source code
|
| .genesInNode |
Source code
|
| .get.all.node.annotation |
Source code
|
| .get.sig.gene.in.term |
Source code
|
| .getFromNode |
Source code
|
| .getGeneData |
Source code
|
| .getTermsDefinition |
Source code
|
| .onAttach |
Source code
|
| .printGeneData |
Source code
|
| .printTopONTresult |
Source code
|
| .printtopONTdata |
Source code
|
| .printtopONTresultGSEAresult |
Source code
|
| .ps2eps |
Source code
|
| .samepleRunHDO |
Source code
|
| .sigGroups.LEA |
Source code
|
| .sigGroups.classic |
Source code
|
| .sigGroups.classicGsea |
Source code
|
| .sigGroups.elim |
Source code
|
| .sigGroups.gseaElim |
Source code
|
| .sigGroups.parentChild |
Source code
|
| .sigGroups.weight |
Source code
|
| .sigGroups.weight01 |
Source code
|
| .sigRatio.01 |
Source code
|
| .sigRatio.log |
Source code
|
| .sigRatio.ratio |
Source code
|
| .writeToNodes |
Source code
|
| Determines the levels of a Directed Acyclic Graph (DAG) |
Man page
|
| GOFisherTest |
Man page
|
| GOFisherTest,classicCount-method |
Man page
|
| GOFisherTest,elimCount-method |
Man page
|
| GOKSTest |
Man page
|
| GOKSTest,classicScore-method |
Man page
|
| GOKSTiesTest |
Man page
|
| GOKSTiesTest,classicScore-method |
Man page
|
| GOSumTest |
Man page
|
| GOSumTest,classicScore-method |
Man page
|
| GOdata |
Man page
|
| GOglobalTest |
Man page
|
| GOglobalTest,classicExpr-method |
Man page
|
| GOplot |
Man page
Source code
|
| GOplot.batch |
Source code
|
| GOplot.counts |
Source code
|
| GOtTest |
Man page
|
| GOtTest,classicScore-method |
Man page
|
| GSEA.EnrichmentScore.weighted |
Source code
|
| GSEA.EnrichmentScore.weighted.batch |
Source code
|
| GSEA.GeneRanking |
Source code
|
| GSEA.HeatMapPlot |
Source code
|
| GenTable |
Man page
|
| GenTable,topONTdata-method |
Man page
|
| Gene set tests statistics |
Man page
|
| Name |
Man page
|
| Name,groupStats-method |
Man page
|
| Name,weightCount-method |
Man page
|
| Name<- |
Man page
|
| Name<-,groupStats-method |
Man page
|
| ONTdata |
Man page
|
| Term |
Man page
|
| Weights |
Man page
|
| Weights,weightCount,logical-method |
Man page
|
| Weights,weightCount,missing-method |
Man page
|
| Weights,weightCount-method |
Man page
|
| Weights<- |
Man page
|
| Weights<-,weightCount-method |
Man page
|
| algorithm |
Man page
Man page
|
| algorithm,topGOresult-method |
Man page
Man page
|
| algorithm<- |
Man page
Man page
|
| algorithm<-,topGOresult-method |
Man page
Man page
|
| allGenes |
Man page
Man page
|
| allGenes,topGOdata-method |
Man page
|
| allGenes,topONTdata-method |
Man page
|
| allMembers |
Man page
|
| allMembers,elimScore-method |
Man page
|
| allMembers,groupStats-method |
Man page
|
| allMembers,parentChild-method |
Man page
|
| allMembers,weight01Expr-method |
Man page
|
| allMembers,weight01Score-method |
Man page
|
| allMembers,weightCount-method |
Man page
|
| allMembers<- |
Man page
|
| allMembers<-,classicExpr-method |
Man page
|
| allMembers<-,groupStats-method |
Man page
|
| allMembers<-,pC-method |
Man page
|
| allMembers<-,parentChild-method |
Man page
|
| allParents |
Man page
|
| allParents,parentChild-method |
Man page
|
| allRes |
Man page
|
| allScore |
Man page
|
| allScore,classicScore,logical-method |
Man page
|
| allScore,classicScore,missing-method |
Man page
|
| allScore,elimScore,logical-method |
Man page
|
| allScore,elimScore,missing-method |
Man page
|
| allScore,weight01Score,logical-method |
Man page
|
| allScore,weight01Score,missing-method |
Man page
|
| alternative,elimScore-method |
Man page
|
| annFUN |
Man page
Source code
|
| annFUN.GO2genes |
Man page
Source code
|
| annFUN.db |
Man page
Source code
|
| annFUN.file |
Man page
Source code
|
| annFUN.gene2GO |
Man page
Source code
|
| annFUN.gene2GO.Score |
Source code
|
| annFUN.org |
Man page
Source code
|
| attrInTerm |
Man page
Man page
|
| attrInTerm,topGOdata,character,character-method |
Man page
|
| attrInTerm,topGOdata,character,missing-method |
Man page
|
| attrInTerm,topONTdata,character,character-method |
Man page
|
| attrInTerm,topONTdata,character,missing-method |
Man page
|
| buildGOgraph.topology |
Source code
|
| buildLevels |
Man page
Source code
|
| classicCount-class |
Man page
|
| classicExpr-class |
Man page
|
| classicScore-class |
Man page
|
| combineResults |
Man page
Man page
Source code
|
| contTable |
Man page
|
| contTable,classicCount-method |
Man page
|
| contTable,elimCount-method |
Man page
|
| countGenesInTerm |
Man page
Man page
|
| countGenesInTerm,topGOdata,character-method |
Man page
|
| countGenesInTerm,topGOdata,missing-method |
Man page
|
| countGenesInTerm,topONTdata,character-method |
Man page
|
| countGenesInTerm,topONTdata,missing-method |
Man page
|
| cutOff |
Man page
|
| cutOff,elimCount-method |
Man page
|
| cutOff,elimExpr-method |
Man page
|
| cutOff,elimScore-method |
Man page
|
| cutOff<- |
Man page
|
| cutOff<-,elimCount-method |
Man page
|
| cutOff<-,elimExpr-method |
Man page
|
| cutOff<-,elimScore-method |
Man page
|
| cutoff.result |
Source code
|
| depth |
Man page
|
| depth,leaCount-method |
Man page
|
| depth,leaExpr-method |
Man page
|
| depth,leaScore-method |
Man page
|
| depth<- |
Man page
|
| depth<-,leaCount-method |
Man page
|
| depth<-,leaExpr-method |
Man page
|
| depth<-,leaScore-method |
Man page
|
| description |
Man page
Man page
|
| description,topGOdata-method |
Man page
|
| description,topGOresult-method |
Man page
Man page
|
| description,topONTdata-method |
Man page
|
| description<- |
Man page
Man page
|
| description<-,topGOdata,ANY-method |
Man page
|
| description<-,topGOresult,ANY-method |
Man page
Man page
|
| description<-,topONTdata,ANY-method |
Man page
|
| diagnosticMethods |
Man page
|
| elim |
Man page
|
| elim,elimCount-method |
Man page
|
| elim,elimScore-method |
Man page
|
| elim,weight01Count-method |
Man page
|
| elim,weight01Expr-method |
Man page
|
| elim,weight01Score-method |
Man page
|
| elim<- |
Man page
|
| elim<-,elimCount-method |
Man page
|
| elim<-,elimScore-method |
Man page
|
| elim<-,weight01Count-method |
Man page
|
| elim<-,weight01Expr-method |
Man page
|
| elim<-,weight01Score-method |
Man page
|
| elimCount-class |
Man page
|
| elimExpr-class |
Man page
|
| elimScore-class |
Man page
|
| emptyExpr,classicExpr-method |
Man page
|
| expressionMatrix |
Man page
Man page
|
| expressionMatrix,topGOdata-method |
Man page
|
| expressionMatrix,topONTdata-method |
Man page
|
| feasible |
Man page
Man page
|
| feasible,topGOdata-method |
Man page
|
| feasible,topONTdata-method |
Man page
|
| feasible<- |
Man page
Man page
|
| feasible<-,topGOdata-method |
Man page
|
| feasible<-,topONTdata-method |
Man page
|
| feasibleGenes.db |
Source code
|
| filter.ontology.annotation |
Source code
|
| geneData |
Man page
Man page
|
| geneData,topGOresult-method |
Man page
Man page
|
| geneData<- |
Man page
Man page
|
| geneData<-,topGOresult-method |
Man page
Man page
|
| geneID2TERM |
Man page
|
| geneList |
Man page
|
| geneNames |
Man page
|
| geneScore |
Man page
Man page
|
| geneScore,topGOdata,character-method |
Man page
|
| geneScore,topGOdata,missing-method |
Man page
|
| geneScore,topGOdata-method |
Man page
|
| geneScore,topONTdata,character-method |
Man page
|
| geneScore,topONTdata,missing-method |
Man page
|
| geneScore,topONTdata-method |
Man page
|
| geneSelectionFun |
Man page
Man page
|
| geneSelectionFun,topGOdata-method |
Man page
|
| geneSelectionFun,topONTdata-method |
Man page
|
| geneSelectionFun<- |
Man page
Man page
|
| geneSelectionFun<-,topGOdata-method |
Man page
|
| geneSelectionFun<-,topONTdata-method |
Man page
|
| genes |
Man page
Man page
|
| genes,topGOdata-method |
Man page
|
| genes,topONTdata-method |
Man page
|
| genesInTerm |
Man page
Man page
|
| genesInTerm,topGOdata,character-method |
Man page
|
| genesInTerm,topGOdata,missing-method |
Man page
|
| genesInTerm,topONTdata,character-method |
Man page
|
| genesInTerm,topONTdata,missing-method |
Man page
|
| getGeneOntologyAnnotation |
Source code
|
| getGraphRoot |
Man page
Source code
|
| getNoOfLevels |
Man page
Source code
|
| getPvalues |
Man page
Source code
|
| getSigGroups |
Man page
|
| getSigGroups,topONTdata,classicCount-method |
Man page
|
| getSigGroups,topONTdata,classicExpr-method |
Man page
|
| getSigGroups,topONTdata,classicScore-method |
Man page
|
| getSigGroups,topONTdata,elimCount-method |
Man page
|
| getSigGroups,topONTdata,elimExpr-method |
Man page
|
| getSigGroups,topONTdata,elimScore-method |
Man page
|
| getSigGroups,topONTdata,leaCount-method |
Man page
|
| getSigGroups,topONTdata,leaExpr-method |
Man page
|
| getSigGroups,topONTdata,leaScore-method |
Man page
|
| getSigGroups,topONTdata,pC-method |
Man page
|
| getSigGroups,topONTdata,parentChild-method |
Man page
|
| getSigGroups,topONTdata,weight01Count-method |
Man page
|
| getSigGroups,topONTdata,weight01Expr-method |
Man page
|
| getSigGroups,topONTdata,weight01Score-method |
Man page
|
| getSigGroups,topONTdata,weightCount-method |
Man page
|
| getSigGroups-methods |
Man page
|
| getSigRatio |
Man page
|
| getSigRatio,weightCount-method |
Man page
|
| graph |
Man page
Man page
|
| graph,topGOdata-method |
Man page
|
| graph,topONTdata-method |
Man page
|
| graph<- |
Man page
Man page
|
| graph<-,topGOdata-method |
Man page
|
| graph<-,topONTdata-method |
Man page
|
| groupGOTerms |
Source code
|
| groupStats-class |
Man page
|
| inducedGraph |
Man page
Source code
|
| init |
Man page
Source code
|
| initONT |
Man page
Source code
|
| initWHAT |
Man page
Source code
|
| initialize,classicCount-method |
Man page
|
| initialize,classicExpr-method |
Man page
|
| initialize,classicScore-method |
Man page
|
| initialize,elimCount-method |
Man page
|
| initialize,elimExpr-method |
Man page
|
| initialize,elimScore-method |
Man page
|
| initialize,groupStats-method |
Man page
|
| initialize,leaCount-method |
Man page
|
| initialize,leaExpr-method |
Man page
|
| initialize,leaScore-method |
Man page
|
| initialize,pC-method |
Man page
|
| initialize,parentChild-method |
Man page
|
| initialize,topGOdata-method |
Man page
|
| initialize,topGOresult-method |
Man page
Man page
|
| initialize,topONTdata-method |
Man page
|
| initialize,weight01Count-method |
Man page
|
| initialize,weight01Expr-method |
Man page
|
| initialize,weight01Score-method |
Man page
|
| initialize,weightCount-method |
Man page
|
| inverseList |
Man page
Source code
|
| joinFun |
Man page
|
| joinFun,parentChild-method |
Man page
|
| leaCount-class |
Man page
|
| leaExpr-class |
Man page
|
| leaScore-class |
Man page
|
| list.annotation |
Source code
|
| list.reference |
Source code
|
| mapAnnotationToSpecies.fly |
Source code
|
| mapAnnotationToSpecies.score.fly |
Source code
|
| mapGenes2GOgraph |
Source code
|
| mapGenes2GOgraph2 |
Source code
|
| members |
Man page
|
| members,elimScore-method |
Man page
|
| members,groupStats,missing-method |
Man page
|
| members,weight01Expr,missing-method |
Man page
|
| members,weight01Score,missing-method |
Man page
|
| members,weightCount-method |
Man page
|
| members<- |
Man page
|
| members<-,groupStats-method |
Man page
|
| membersExpr |
Man page
|
| membersExpr,classicExpr-method |
Man page
|
| membersScore |
Man page
|
| membersScore,classicScore-method |
Man page
|
| membersScore,elimScore-method |
Man page
|
| membersScore,weight01Score-method |
Man page
|
| myInterestingGenes |
Man page
|
| nodesInInducedGraph |
Man page
Source code
|
| nodesInInducedGraph2 |
Source code
|
| numAllMembers |
Man page
|
| numAllMembers,elimCount-method |
Man page
|
| numAllMembers,elimScore-method |
Man page
|
| numAllMembers,groupStats-method |
Man page
|
| numAllMembers,parentChild-method |
Man page
|
| numAllMembers,weight01Count-method |
Man page
|
| numAllMembers,weight01Expr-method |
Man page
|
| numAllMembers,weight01Score-method |
Man page
|
| numAllMembers,weightCount-method |
Man page
|
| numGenes |
Man page
Man page
|
| numGenes,topGOdata-method |
Man page
|
| numGenes,topONTdata-method |
Man page
|
| numMembers |
Man page
|
| numMembers,elimCount-method |
Man page
|
| numMembers,elimScore-method |
Man page
|
| numMembers,groupStats-method |
Man page
|
| numMembers,weight01Count-method |
Man page
|
| numMembers,weight01Expr-method |
Man page
|
| numMembers,weight01Score-method |
Man page
|
| numMembers,weightCount-method |
Man page
|
| numSigAll |
Man page
|
| numSigAll,classicCount-method |
Man page
|
| numSigAll,elimCount-method |
Man page
|
| numSigAll,parentChild-method |
Man page
|
| numSigAll,weight01Count-method |
Man page
|
| numSigAll,weightCount-method |
Man page
|
| numSigGenes |
Man page
Man page
|
| numSigGenes,topGOdata-method |
Man page
|
| numSigGenes,topONTdata-method |
Man page
|
| numSigMembers |
Man page
|
| numSigMembers,classicCount-method |
Man page
|
| numSigMembers,elimCount-method |
Man page
|
| numSigMembers,weight01Count-method |
Man page
|
| numSigMembers,weightCount-method |
Man page
|
| ontology |
Man page
Man page
|
| ontology,topGOdata-method |
Man page
|
| ontology,topONTdata-method |
Man page
|
| ontology<- |
Man page
Man page
|
| ontology<-,topGOdata-method |
Man page
|
| ontology<-,topONTdata-method |
Man page
|
| pC-class |
Man page
|
| pType |
Man page
|
| pType,classicExpr-method |
Man page
|
| pType<- |
Man page
|
| pType<-,classicExpr-method |
Man page
|
| parentChild-class |
Man page
|
| parseGeneOntologyAnnotation |
Source code
|
| penalise |
Man page
|
| penalise,weightCount,numeric,numeric-method |
Man page
|
| permSumStats |
Man page
Source code
|
| permSumStats.all |
Man page
Source code
|
| phenotype |
Man page
Man page
|
| phenotype,topGOdata-method |
Man page
|
| phenotype,topONTdata-method |
Man page
|
| plot.result |
Source code
|
| print,topGOdata-method |
Man page
|
| print,topGOresult-method |
Man page
Man page
|
| print,topONTdata-method |
Man page
|
| printDOT |
Source code
|
| printGenes |
Man page
|
| printGenes,topONTdata,character,character-method |
Man page
|
| printGenes,topONTdata,character,missing-method |
Man page
|
| printGenes-methods |
Man page
|
| printGraph |
Man page
|
| printGraph,topONTdata,topGOresult,numeric,missing-method |
Man page
|
| printGraph,topONTdata,topGOresult,numeric,topGOresult-method |
Man page
|
| printGraph-methods |
Man page
|
| rankMembers |
Man page
|
| rankMembers,classicScore-method |
Man page
|
| rankMembers,elimScore-method |
Man page
|
| rankMembers,weight01Score-method |
Man page
|
| read.cls |
Source code
|
| read.gct |
Source code
|
| read.gmt |
Source code
|
| readMappings |
Man page
Source code
|
| readMappingswithScore |
Source code
|
| reorder.result |
Source code
|
| resultElimFis |
Man page
|
| resultFis |
Man page
|
| reverseArch |
Man page
Source code
|
| revmapWithScore |
Source code
|
| roundFun |
Man page
|
| roundFun,weightCount-method |
Man page
|
| run.batch |
Source code
|
| runTest |
Man page
|
| runTest,groupStats,missing,missing-method |
Man page
|
| runTest,groupStats-method |
Man page
|
| runTest,topONTdata,character,character-method |
Man page
|
| runTest,topONTdata,missing,character-method |
Man page
|
| score |
Man page
Man page
|
| score,topGOresult-method |
Man page
Man page
|
| score<- |
Man page
|
| score<-,classicScore-method |
Man page
|
| score<-,elimScore-method |
Man page
|
| score<-,topGOresult-method |
Man page
Man page
|
| scoreOrder |
Man page
|
| scoreOrder,classicScore-method |
Man page
|
| scoresInTerm |
Man page
Man page
|
| scoresInTerm,topGOdata,character-method |
Man page
|
| scoresInTerm,topGOdata,missing-method |
Man page
|
| scoresInTerm,topONTdata,character-method |
Man page
|
| scoresInTerm,topONTdata,missing-method |
Man page
|
| search.result |
Source code
|
| show,topGOdata-method |
Man page
|
| show,topGOresult-method |
Man page
Man page
|
| show,topONTdata-method |
Man page
|
| showGroupDensity |
Man page
Source code
|
| showSigOfNodes |
Man page
Source code
|
| showSigOfNodes.batch |
Source code
|
| sigAllMembers |
Man page
|
| sigAllMembers,classicCount-method |
Man page
|
| sigAllMembers,elimCount-method |
Man page
|
| sigAllMembers,parentChild-method |
Man page
|
| sigAllMembers,weight01Count-method |
Man page
|
| sigGenes |
Man page
Man page
|
| sigGenes,topGOdata-method |
Man page
|
| sigGenes,topONTdata-method |
Man page
|
| sigMembers |
Man page
|
| sigMembers,classicCount-method |
Man page
|
| sigMembers,elimCount-method |
Man page
|
| sigMembers,weight01Count-method |
Man page
|
| sigMembers<- |
Man page
|
| sigMembers<-,classicCount-method |
Man page
|
| sigMembers<-,elimCount-method |
Man page
|
| sigMembers<-,pC-method |
Man page
|
| sigMembers<-,parentChild-method |
Man page
|
| sigRatio |
Man page
|
| sigRatio,weightCount-method |
Man page
|
| sigRatio<- |
Man page
|
| sigRatio<-,weightCount-method |
Man page
|
| significant |
Man page
|
| significant,weightCount-method |
Man page
|
| termStat |
Man page
Man page
|
| termStat,topGOdata,character-method |
Man page
|
| termStat,topGOdata,missing-method |
Man page
|
| termStat,topONTdata,character-method |
Man page
|
| termStat,topONTdata,missing-method |
Man page
|
| testName |
Man page
Man page
|
| testName,topGOresult-method |
Man page
Man page
|
| testName<- |
Man page
Man page
|
| testName<-,topGOresult-method |
Man page
Man page
|
| testStatPar |
Man page
|
| testStatPar,groupStats-method |
Man page
|
| testStatPar,weightCount-method |
Man page
|
| testStatistic |
Man page
|
| testStatistic,groupStats-method |
Man page
|
| testStatistic,weightCount-method |
Man page
|
| to.latex.table |
Source code
|
| topGOdata-class |
Man page
|
| topGOresult-class |
Man page
Man page
|
| topONTdata-class |
Man page
|
| topOnto |
Man page
|
| topOnto-package |
Man page
|
| updateGenes |
Man page
Man page
|
| updateGenes,topGOdata,factor,missing-method |
Man page
|
| updateGenes,topGOdata,numeric,function-method |
Man page
|
| updateGenes,topONTdata,factor,missing-method |
Man page
|
| updateGenes,topONTdata,numeric,function-method |
Man page
|
| updateGroup |
Man page
|
| updateGroup,groupStats,character,character-method |
Man page
|
| updateGroup,pC,missing,character-method |
Man page
|
| updateGroup,pC,missing,missing-method |
Man page
|
| updateGroup,parentChild,missing,character-method |
Man page
|
| updateGroup,weightCount,character,character-method |
Man page
|
| updateTerm<- |
Man page
Man page
|
| updateTerm<-,topGOdata,character-method |
Man page
|
| updateTerm<-,topONTdata,character-method |
Man page
|
| usedGO |
Man page
Man page
|
| usedGO,topGOdata-method |
Man page
|
| usedGO,topONTdata-method |
Man page
|
| weight01Count-class |
Man page
|
| weight01Expr-class |
Man page
|
| weight01Score-class |
Man page
|
| weightCount-class |
Man page
|
| whichAlgorithms |
Man page
Source code
|
| whichTests |
Man page
Source code
|
| write.gmt |
Source code
|
