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
