benomylsetup            A test dataset for goCluster
checkData               Checks if a variable contains data
checkProtection         A function to protect intermediate results
                        from being overwritten
checkannotationpackage
                        Check if an annotation package contains the
                        specified environment.
clusterAlgorithm-class
                        Class "clusterAlgorithm"
clusterAlgorithmClara-class
                        Class "clusterAlgorithmClara", provides
                        partitioning around medoids of large datasets
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.
clusterAnnotation-class
                        Class "clusterAnnotation", an abstract class
                        that represents functions for annotating
                        microarray datasets.
clusterAnnotationChromosome-abp-class
                        Class "clusterAnnotationChromosome-abp",
                        prepares the chromosome annotation for
                        subsequent statistical analysis.
clusterAnnotationGO-abp-class
                        Class "clusterAnnotationGO-abp", prepares the
                        GO annotation for subsequent statistical
                        analysis.
clusterData-class       Class "clusterData", a class for holding
                        datasets that are going to be analysed with
                        goCluster.
clusterModule-class     Class "clusterModule" represents the base
                        class for all goCluster objects
clusterSignif-class     Class "clusterSignif"
clusterSignifBase-class
                        Class "clusterSignifBase"
clusterSignifBonferroni-class
                        Class "clusterSignifBonferroni"
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"
clusterVisualHeatmap-class
                        Class "clusterVisualHeatmap", prepares a
                        goCluster analysis for visualization.
clusterVisualNone-class
                        Class "clusterVisualNone", a placeholder for
                        the goCluster visualization methods
clusterclara            Clusters a dataset with the clara function
clusterhclust           Clusters a dataset using hierarchical
                        clustering
clusterkmeans           Clusters a dataset with the kmeans function
clusterpam              Clusters a dataset with the pam function
config                  Interactively configure a goCluster-module
convertlist             Function to convert user input into a
                        character vector
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
goCluster-class         Class "goCluster", a class for combining
                        clustering results with functional annotation
groupCount              Count the number of clusters
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
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
