| allGenes |
Class "topGOdata" |
| allGenes,topGOdata-method |
Class "topGOdata" |
| allMembers |
Class "groupStats" |
| allMembers,elimScore-method |
Class "elimScore" |
| allMembers,groupStats-method |
Class "groupStats" |
| allMembers,weightCount-method |
Class "weightCount" |
| allMembers<-,groupStats-method |
Class "groupStats" |
| allScore |
Class "classicScore" |
| allScore,classicScore,logical-method |
Class "classicScore" |
| allScore,classicScore,missing-method |
Class "classicScore" |
| allScore,elimScore,logical-method |
Class "elimScore" |
| allScore,elimScore,missing-method |
Class "elimScore" |
| alternative,elimScore-method |
Class "elimScore" |
| annFUN.gene2GO |
functions to map gene IDs to GO terms |
| annFUN.GO2genes |
functions to map gene IDs to GO terms |
| annFUN.hgu |
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" |
| 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<-,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 |
Determines the levels of a Directed Acyclic Graph (DAG) |
| getNoOfLevels |
Determines the levels of a Directed Acyclic Graph (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,classicScore-method |
Algorithms for scoring GO terms |
| getSigGroups,topGOdata,elimCount-method |
Algorithms for scoring GO terms |
| getSigGroups,topGOdata,elimScore-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 |
Fischer's exact test for gene set |
| GOFisherTest,classicCount-method |
Class "classicCount" |
| GOFisherTest,elimCount-method |
Class "elimCount" |
| GOKSTest |
Kolmogorov-Smirnov test for gene sets |
| GOKSTest,classicScore-method |
Class "classicScore" |
| GOKSTest,elimScore-method |
Class "elimScore" |
| GOMFTerm |
~~function to do ... ~~ |
| GOplot |
~~ Methods for Function printGraph in Package ‘topGO’ ~~ |
| GOtTest |
Kolmogorov-Smirnov test for gene sets |
| GOtTest,classicScore-method |
Class "classicScore" |
| graph |
Class "topGOdata" |
| graph,topGOdata-method |
Class "topGOdata" |
| graph<-,topGOdata-method |
Class "topGOdata" |
| groupGOTerms |
~~function to do ... ~~ |
| groupStats-class |
Class "groupStats" |
| Name |
Class "groupStats" |
| Name,groupStats-method |
Class "groupStats" |
| Name,weightCount-method |
Class "weightCount" |
| Name<-,groupStats-method |
Class "groupStats" |
| numAllMembers |
Class "groupStats" |
| numAllMembers,elimCount-method |
Class "elimCount" |
| numAllMembers,elimScore-method |
Class "elimScore" |
| numAllMembers,groupStats-method |
Class "groupStats" |
| numAllMembers,weightCount-method |
Class "weightCount" |
| numGenes |
Class "topGOdata" |
| numGenes,topGOdata-method |
Class "topGOdata" |
| numMembers |
Class "groupStats" |
| numMembers,elimCount-method |
Class "elimCount" |
| numMembers,elimScore-method |
Class "elimScore" |
| numMembers,groupStats-method |
Class "groupStats" |
| numMembers,weightCount-method |
Class "weightCount" |
| numSigAll |
Class "classicCount" |
| numSigAll,classicCount-method |
Class "classicCount" |
| numSigAll,elimCount-method |
Class "elimCount" |
| numSigAll,weightCount-method |
Class "weightCount" |
| numSigGenes |
Class "topGOdata" |
| numSigGenes,topGOdata-method |
Class "topGOdata" |
| numSigMembers |
Class "classicCount" |
| numSigMembers,classicCount-method |
Class "classicCount" |
| numSigMembers,elimCount-method |
Class "elimCount" |
| numSigMembers,weightCount-method |
Class "weightCount" |
| penalise |
Class "weightCount" |
| penalise,weightCount,numeric,numeric-method |
Class "weightCount" |
| phenotype |
Class "topGOdata" |
| phenotype,topGOdata-method |
Class "topGOdata" |
| print,topGOdata-method |
Class "topGOdata" |
| 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’ ~~ |
| score |
Class "topGOresult" |
| score,topGOresult-method |
Class "topGOresult" |
| score<-,classicScore-method |
Class "classicScore" |
| score<-,elimScore-method |
Class "elimScore" |
| 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" |
| showSigOfNodes |
~~ Methods for Function printGraph in Package ‘topGO’ ~~ |
| sigAllMembers |
Class "classicCount" |
| sigAllMembers,classicCount-method |
Class "classicCount" |
| sigAllMembers,elimCount-method |
Class "elimCount" |
| sigGenes |
Class "topGOdata" |
| sigGenes,topGOdata-method |
Class "topGOdata" |
| sigMembers |
Class "classicCount" |
| sigMembers,classicCount-method |
Class "classicCount" |
| sigMembers,elimCount-method |
Class "elimCount" |
| sigMembers<-,classicCount-method |
Class "classicCount" |
| sigMembers<-,elimCount-method |
Class "elimCount" |
| significant |
Class "weightCount" |
| significant,weightCount-method |
Class "weightCount" |
| sigRatio |
Class "weightCount" |
| sigRatio,weightCount-method |
Class "weightCount" |
| sigRatio<-,weightCount-method |
Class "weightCount" |