Function	Description
benomylsetup	A test dataset for goCluster
checkannotationpackage	Check if an annotation package contains the specified environment.
checkData	Checks if a variable contains data.
checkProtection	A function to protect intermediate results from being overwritten
clusterAlgorithmClara-class	Class "clusterAlgorithmClara", provides partitioning around medoids of large datasets
clusterAlgorithm-class	Class "clusterAlgorithm"
clusterAlgorithmHclust-class	Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.
clusterAlgorithmKmeans-class	Class "clusterAlgorithmKmeans", provides kmeans clustering for goCluster.
clusterAlgorithmPam-class	Class "clusterAlgorithmPam", provides partitioning around medoids for goCluster.
clusterAnnotationChromosome-abp-class	Class "clusterAnnotationChromosome-abp", prepares the chromosome annotation for subsequent statistical analysis.
clusterAnnotation-class	Class "clusterAnnotation", an abstract class that represents functions for annotating microarray datasets.
clusterAnnotationGO-abp-class	Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.
clusterclara	Clusters a dataset with the clara function
clusterData-class	Class "clusterData", a class for holding datasets that are going to be analysed with goCluster.
clusterhclust	Clusters a dataset using hierarchical clustering
clusterkmeans	Clusters a dataset with the kmeans function
clusterModule-class	Class "clusterModule" represents the base class for all goCluster objects
clusterpam	Clusters a dataset with the pam function
clusterSignifBase-class	Class "clusterSignifBase"
clusterSignifBonferroni-class	Class "clusterSignifBonferroni"
clusterSignif-class	Class "clusterSignif"
clusterSignifFDR-class	Class "clusterSignifFDR"
clusterStatistic-class	Class "clusterStatistic" provides statistical analysis for goCluster
clusterStatisticHyper-class	Class "clusterStatisticHyper" provides the hypergeometric distribution for the goCluster analysis.
clusterVisual-class	Class "clusterVisual"
clusterVisualHclust-class	Class "clusterVisualHclust" prepares a visualization for a dataset that has been clustered with hierarchical clustering.
clusterVisualHeatmap-class	Class "clusterVisualHeatmap", prepares a goCluster analysis for visualization.
clusterVisualNone-class	Class "clusterVisualNone", a placeholder for the goCluster visualization methods
collectTerms	A function to collect all annotation terms of a tree
config	Interactively configure a goCluster-module
display	Display a visualization module
evalClusterHyper	Evaluates a clustering result with regard to an enrichment of annotation terms in specific clusters.
execute	Executes a goCluster-module
execute<-	Configures and executes a goCluster-module
getChildrenClasses	Get the children of an abstract class
getGeneColors	Returns a set of colors
goCluster-class	Class "goCluster", a class for combining clustering results with functional annotation
groupCount	Count the number of clusters
mergeResult	Merges two lists of selected genes to the selection with minimal p-value
minimizeSelection	Reduces the leaves of a tree to minimal p-values
plotAxis	Plots the axis besides a hierarchical clustering
prepareAxis	Reduces a tree of selected items to a vector of non-overelapping regions with minimal p-value
prepareCHRannotation	A function to prepare the gene localization for subsequent statistical analysis
prepareGOannotation	A function to prepare the gene ontology annotation for subsequent statistical analysis
prepareHeatmap	A function to reformat a goCluster result for graphical representation
printData	Helper printing function
randomizeTree	Select interesting annotation terms after FDR analysis
reset	Reset a goCluster-module
selectChild	Choosing the child of an abstract class
selectCore	A menu function
selectDouble	A menu for choosing a floating point number
selectNumber	A menu for choosing an integer
selectOption	A menu for choosing an option
selectStats	Selects relevant annotation terms
selectStatsBonferroni	Performs Bonferroni correction and subsequently selects relevant annotation terms.
selectTerms	A function to select interesting annotation terms with the associated genes from a goCluster object
setup	Returns the setup of a goCluster-module
setup<-	Configures a goCluster-object by assigning a list of parameters