benomylsetup	benomylsetup
checkannotationpackage	checkannotationpackage
checkchrannotation	checkannotationpackage
checkData	checkData
checkgoannotation	checkannotationpackage
checkProtection	checkProtection
clusterAlgorithm-class	clusterAlgorithm-class
clusterAlgorithmClara-class	clusterAlgorithmClara-class
clusterAlgorithmHclust-class	clusterAlgorithmHclust-class
clusterAlgorithmKmeans-class	clusterAlgorithmKmeans-class
clusterAlgorithmPam-class	clusterAlgorithmPam-class
clusterAnnotation-class	clusterAnnotation-class
clusterAnnotationChromosome-abp-class	clusterAnnotationChromosome-abp-class
clusterAnnotationGO-abp-class	clusterAnnotationGO-abp-class
clusterclara	clusterclara
clusterData-class	clusterData-class
clusterhclust	clusterhclust
clusterkmeans	clusterkmeans
clusterModule-class	clusterModule-class
clusterpam	clusterpam
clusterSignif-class	clusterSignif-class
clusterSignifBase-class	clusterSignifBase-class
clusterSignifBonferroni-class	clusterSignifBonferroni-class
clusterSignifFDR-class	clusterSignifFDR-class
clusterStatistic-class	clusterStatistic-class
clusterStatisticHyper-class	clusterStatisticHyper-class
clusterVisual-class	clusterVisual-class
clusterVisualHeatmap-class	clusterVisualHeatmap-class
clusterVisualNone-class	clusterVisualNone-class
config	config-methods
config,clusterAlgorithm-method	clusterAlgorithm-class
config,clusterAlgorithmClara-method	clusterAlgorithmClara-class
config,clusterAlgorithmHclust-method	clusterAlgorithmHclust-class
config,clusterAlgorithmKmeans-method	clusterAlgorithmKmeans-class
config,clusterAlgorithmPam-method	clusterAlgorithmPam-class
config,clusterAnnotation-method	clusterAnnotation-class
config,clusterAnnotationChromosome-abp-method	clusterAnnotationChromosome-abp-class
config,clusterAnnotationGO-abp-method	clusterAnnotationGO-abp-class
config,clusterData-method	clusterData-class
config,clusterModule-method	clusterModule-class
config,clusterSignif-method	clusterSignif-class
config,clusterSignifBase-method	clusterSignifBase-class
config,clusterSignifBonferroni-method	clusterSignifBonferroni-class
config,clusterSignifFDR-method	clusterSignifFDR-class
config,clusterStatistic-method	clusterStatistic-class
config,clusterStatisticHyper-method	clusterStatisticHyper-class
config,clusterVisual-method	clusterVisual-class
config,clusterVisualHeatmap-method	clusterVisualHeatmap-class
config,clusterVisualNone-method	clusterVisualNone-class
config,goCluster-method	goCluster-class
convertevidence	convertlist
convertlist	convertlist
convertontology	convertlist
evalAnnosetHyper	evalClusterHyper
evalClusterHyper	evalClusterHyper
EVIDENCECODES	clusterAnnotationGO-abp-class
execute	execute-methods
execute,clusterAlgorithm-method	clusterAlgorithm-class
execute,clusterAlgorithmClara-method	clusterAlgorithmClara-class
execute,clusterAlgorithmHclust-method	clusterAlgorithmHclust-class
execute,clusterAlgorithmKmeans-method	clusterAlgorithmKmeans-class
execute,clusterAlgorithmPam-method	clusterAlgorithmPam-class
execute,clusterAnnotation-method	clusterAnnotation-class
execute,clusterAnnotationChromosome-abp-method	clusterAnnotationChromosome-abp-class
execute,clusterAnnotationGO-abp-method	clusterAnnotationGO-abp-class
execute,clusterData-method	clusterData-class
execute,clusterModule-method	clusterModule-class
execute,clusterSignif-method	clusterSignif-class
execute,clusterSignifBase-method	clusterSignifBase-class
execute,clusterSignifBonferroni-method	clusterSignifBonferroni-class
execute,clusterSignifFDR-method	clusterSignifFDR-class
execute,clusterStatistic-method	clusterStatistic-class
execute,clusterStatisticHyper-method	clusterStatisticHyper-class
execute,clusterVisual-method	clusterVisual-class
execute,clusterVisualHeatmap-method	clusterVisualHeatmap-class
execute,clusterVisualNone-method	clusterVisualNone-class
execute<-	execute-assign-methods
execute<-,clusterModule-method	clusterModule-class
getChildrenClasses	getChildrenClasses
goCluster-class	goCluster-class
groupCount	groupCount
HCLUSTDISTANCE	clusterAlgorithmHclust-class
HCLUSTMETHOD	clusterAlgorithmHclust-class
mergeAnno	selectAnnoStats
ONTOLOGIES	clusterAnnotationGO-abp-class
prepareCHRannotation	prepareCHRannotation
prepareGOannotation	prepareGOannotation
prepareHeatmap	prepareHeatmap
randomizeTree	selectAnnoStats
reset	reset-methods
reset,clusterAlgorithm-method	clusterAlgorithm-class
reset,clusterAlgorithmClara-method	clusterAlgorithmClara-class
reset,clusterAlgorithmHclust-method	clusterAlgorithmHclust-class
reset,clusterAlgorithmKmeans-method	clusterAlgorithmKmeans-class
reset,clusterAlgorithmPam-method	clusterAlgorithmPam-class
reset,clusterAnnotation-method	clusterAnnotation-class
reset,clusterAnnotationChromosome-abp-method	clusterAnnotationChromosome-abp-class
reset,clusterAnnotationGO-abp-method	clusterAnnotationGO-abp-class
reset,clusterData-method	clusterData-class
reset,clusterModule-method	clusterModule-class
reset,clusterSignif-method	clusterSignif-class
reset,clusterSignifBase-method	clusterSignifBase-class
reset,clusterSignifBonferroni-method	clusterSignifBonferroni-class
reset,clusterSignifFDR-method	clusterSignifFDR-class
reset,clusterStatistic-method	clusterStatistic-class
reset,clusterStatisticHyper-method	clusterStatisticHyper-class
reset,clusterVisual-method	clusterVisual-class
reset,clusterVisualHeatmap-method	clusterVisualHeatmap-class
reset,goCluster-method	goCluster-class
run,goCluster-method	goCluster-class
run<-,goCluster-method	goCluster-class
selectAnnoStats	selectAnnoStats
selectChild	selectChild
selectCore	selectCore
selectDouble	selectDouble
selectNumber	selectNumber
selectOption	selectOption
selectStats	selectStats
selectStatsBonferroni	selectStatsBonferroni
selectTerms	selectTerms
setup	setup-methods
setup,clusterAlgorithm-method	clusterAlgorithm-class
setup,clusterAlgorithmClara-method	clusterAlgorithmClara-class
setup,clusterAlgorithmHclust-method	clusterAlgorithmHclust-class
setup,clusterAlgorithmKmeans-method	clusterAlgorithmKmeans-class
setup,clusterAlgorithmPam-method	clusterAlgorithmPam-class
setup,clusterAnnotation-method	clusterAnnotation-class
setup,clusterAnnotationChromosome-abp-method	clusterAnnotationChromosome-abp-class
setup,clusterAnnotationGO-abp-method	clusterAnnotationGO-abp-class
setup,clusterData-method	clusterData-class
setup,clusterModule-method	clusterModule-class
setup,clusterSignif-method	clusterSignif-class
setup,clusterSignifBase-method	clusterSignifBase-class
setup,clusterSignifBonferroni-method	clusterSignifBonferroni-class
setup,clusterSignifFDR-method	clusterSignifFDR-class
setup,clusterStatistic-method	clusterStatistic-class
setup,clusterStatisticHyper-method	clusterStatisticHyper-class
setup,clusterVisual-method	clusterVisual-class
setup,clusterVisualHeatmap-method	clusterVisualHeatmap-class
setup,clusterVisualNone-method	clusterVisualNone-class
setup,goCluster-method	goCluster-class
setup<-	setup-assign-methods
setup<-,clusterAlgorithm-method	clusterAlgorithm-class
setup<-,clusterAlgorithmClara-method	clusterAlgorithmClara-class
setup<-,clusterAlgorithmHclust-method	clusterAlgorithmHclust-class
setup<-,clusterAlgorithmKmeans-method	clusterAlgorithmKmeans-class
setup<-,clusterAlgorithmPam-method	clusterAlgorithmPam-class
setup<-,clusterAnnotation-method	clusterAnnotation-class
setup<-,clusterAnnotationChromosome-abp-method	clusterAnnotationChromosome-abp-class
setup<-,clusterAnnotationGO-abp-method	clusterAnnotationGO-abp-class
setup<-,clusterData-method	clusterData-class
setup<-,clusterModule-method	clusterModule-class
setup<-,clusterSignif-method	clusterSignif-class
setup<-,clusterSignifBase-method	clusterSignifBase-class
setup<-,clusterSignifBonferroni-method	clusterSignifBonferroni-class
setup<-,clusterSignifFDR-method	clusterSignifFDR-class
setup<-,clusterStatistic-method	clusterStatistic-class
setup<-,clusterStatisticHyper-method	clusterStatisticHyper-class
setup<-,clusterVisual-method	clusterVisual-class
setup<-,clusterVisualHeatmap-method	clusterVisualHeatmap-class
setup<-,clusterVisualNone-method	clusterVisualNone-class
setup<-,goCluster-method	goCluster-class
