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 |
Class "classicScore" |
alternative,classicScore-method |
Class "classicScore" |
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" |
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" |