Entry: benomylsetup
Aliases: benomylsetup
Keywords: datasets
Description: A test dataset for goCluster
URL: ../../../library/goCluster/html/benomylsetup.html

Entry: checkData
Aliases: checkData
Keywords: utilities
Description: Checks if a variable contains data
URL: ../../../library/goCluster/html/checkData.html

Entry: checkProtection
Aliases: checkProtection
Keywords: utilities
Description: A function to protect intermediate results from being overwritten
URL: ../../../library/goCluster/html/checkProtection.html

Entry: checkannotationpackage
Aliases: checkannotationpackage checkgoannotation checkchrannotation
Keywords: utilities
Description: Check if an annotation package contains the specified environment.
URL: ../../../library/goCluster/html/checkannotationpackage.html

Entry: clusterAlgorithm-class
Aliases: clusterAlgorithm-class config,clusterAlgorithm-method execute,clusterAlgorithm-method reset,clusterAlgorithm-method setup<-,clusterAlgorithm-method setup,clusterAlgorithm-method
Keywords: classes
Description: Class "clusterAlgorithm"
URL: ../../../library/goCluster/html/clusterAlgorithm-class.html

Entry: clusterAlgorithmClara-class
Aliases: clusterAlgorithmClara-class config,clusterAlgorithmClara-method execute,clusterAlgorithmClara-method reset,clusterAlgorithmClara-method setup<-,clusterAlgorithmClara-method setup,clusterAlgorithmClara-method
Keywords: cluster
Description: Class "clusterAlgorithmClara", provides partitioning around medoids of large datasets
URL: ../../../library/goCluster/html/clusterAlgorithmClara-class.html

Entry: clusterAlgorithmHclust-class
Aliases: HCLUSTMETHOD HCLUSTDISTANCE clusterAlgorithmHclust-class config,clusterAlgorithmHclust-method execute,clusterAlgorithmHclust-method reset,clusterAlgorithmHclust-method setup<-,clusterAlgorithmHclust-method setup,clusterAlgorithmHclust-method
Keywords: classes
Description: Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.
URL: ../../../library/goCluster/html/clusterAlgorithmHclust-class.html

Entry: clusterAlgorithmKmeans-class
Aliases: clusterAlgorithmKmeans-class config,clusterAlgorithmKmeans-method execute,clusterAlgorithmKmeans-method reset,clusterAlgorithmKmeans-method setup<-,clusterAlgorithmKmeans-method setup,clusterAlgorithmKmeans-method
Keywords: cluster
Description: Class "clusterAlgorithmKmeans", provides kmeans clustering for goCluster.
URL: ../../../library/goCluster/html/clusterAlgorithmKmeans-class.html

Entry: clusterAlgorithmPam-class
Aliases: clusterAlgorithmPam-class config,clusterAlgorithmPam-method execute,clusterAlgorithmPam-method reset,clusterAlgorithmPam-method setup<-,clusterAlgorithmPam-method setup,clusterAlgorithmPam-method
Keywords: cluster
Description: Class "clusterAlgorithmPam", provides partitioning around medoids for goCluster.
URL: ../../../library/goCluster/html/clusterAlgorithmPam-class.html

Entry: clusterAnnotation-class
Aliases: clusterAnnotation-class config,clusterAnnotation-method execute,clusterAnnotation-method reset,clusterAnnotation-method setup<-,clusterAnnotation-method setup,clusterAnnotation-method
Keywords: classes
Description: Class "clusterAnnotation", an abstract class that represents functions for annotating microarray datasets.
URL: ../../../library/goCluster/html/clusterAnnotation-class.html

Entry: clusterAnnotationChromosome-abp-class
Aliases: clusterAnnotationChromosome-abp-class config,clusterAnnotationChromosome-abp-method execute,clusterAnnotationChromosome-abp-method reset,clusterAnnotationChromosome-abp-method setup<-,clusterAnnotationChromosome-abp-method setup,clusterAnnotationChromosome-abp-method
Keywords: classes
Description: Class "clusterAnnotationChromosome-abp", prepares the chromosome annotation for subsequent statistical analysis.
URL: ../../../library/goCluster/html/clusterAnnotationChromosome-abp-class.html

Entry: clusterAnnotationGO-abp-class
Aliases: clusterAnnotationGO-abp-class config,clusterAnnotationGO-abp-method execute,clusterAnnotationGO-abp-method reset,clusterAnnotationGO-abp-method setup<-,clusterAnnotationGO-abp-method setup,clusterAnnotationGO-abp-method EVIDENCECODES ONTOLOGIES
Keywords: classes
Description: Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.
URL: ../../../library/goCluster/html/clusterAnnotationGO-abp-class.html

Entry: clusterData-class
Aliases: clusterData-class config,clusterData-method execute,clusterData-method reset,clusterData-method setup<-,clusterData-method setup,clusterData-method
Keywords: classes
Description: Class "clusterData", a class for holding datasets that are going to be analysed with goCluster.
URL: ../../../library/goCluster/html/clusterData-class.html

Entry: clusterModule-class
Aliases: clusterModule-class config,clusterModule-method execute,clusterModule-method execute<-,clusterModule-method reset,clusterModule-method setup,clusterModule-method setup<-,clusterModule-method
Keywords: classes
Description: Class "clusterModule" represents the base class for all goCluster objects
URL: ../../../library/goCluster/html/clusterModule-class.html

Entry: clusterSignif-class
Aliases: clusterSignif-class config,clusterSignif-method execute,clusterSignif-method reset,clusterSignif-method setup<-,clusterSignif-method setup,clusterSignif-method
Keywords: classes
Description: Class "clusterSignif"
URL: ../../../library/goCluster/html/clusterSignif-class.html

Entry: clusterSignifBase-class
Aliases: clusterSignifBase-class config,clusterSignifBase-method execute,clusterSignifBase-method reset,clusterSignifBase-method setup<-,clusterSignifBase-method setup,clusterSignifBase-method
Keywords: classes
Description: Class "clusterSignifBase"
URL: ../../../library/goCluster/html/clusterSignifBase-class.html

Entry: clusterSignifBonferroni-class
Aliases: clusterSignifBonferroni-class config,clusterSignifBonferroni-method execute,clusterSignifBonferroni-method reset,clusterSignifBonferroni-method setup<-,clusterSignifBonferroni-method setup,clusterSignifBonferroni-method
Keywords: classes
Description: Class "clusterSignifBonferroni"
URL: ../../../library/goCluster/html/clusterSignifBonferroni-class.html

Entry: clusterSignifFDR-class
Aliases: clusterSignifFDR-class config,clusterSignifFDR-method execute,clusterSignifFDR-method reset,clusterSignifFDR-method setup<-,clusterSignifFDR-method setup,clusterSignifFDR-method
Keywords: classes
Description: Class "clusterSignifFDR"
URL: ../../../library/goCluster/html/clusterSignifFDR-class.html

Entry: clusterStatistic-class
Aliases: clusterStatistic-class config,clusterStatistic-method execute,clusterStatistic-method reset,clusterStatistic-method setup<-,clusterStatistic-method setup,clusterStatistic-method
Keywords: classes
Description: Class "clusterStatistic" provides statistical analysis for goCluster
URL: ../../../library/goCluster/html/clusterStatistic-class.html

Entry: clusterStatisticHyper-class
Aliases: clusterStatisticHyper-class config,clusterStatisticHyper-method execute,clusterStatisticHyper-method reset,clusterStatisticHyper-method setup<-,clusterStatisticHyper-method setup,clusterStatisticHyper-method
Keywords: classes
Description: Class "clusterStatisticHyper" provides the hypergeometric distribution for the goCluster analysis.
URL: ../../../library/goCluster/html/clusterStatisticHyper-class.html

Entry: clusterVisual-class
Aliases: clusterVisual-class config,clusterVisual-method execute,clusterVisual-method reset,clusterVisual-method setup<-,clusterVisual-method setup,clusterVisual-method
Keywords: classes
Description: Class "clusterVisual"
URL: ../../../library/goCluster/html/clusterVisual-class.html

Entry: clusterVisualHeatmap-class
Aliases: clusterVisualHeatmap-class config,clusterVisualHeatmap-method execute,clusterVisualHeatmap-method reset,clusterVisualHeatmap-method setup<-,clusterVisualHeatmap-method setup,clusterVisualHeatmap-method
Keywords: classes
Description: Class "clusterVisualHeatmap", prepares a goCluster analysis for visualization.
URL: ../../../library/goCluster/html/clusterVisualHeatmap-class.html

Entry: clusterVisualNone-class
Aliases: clusterVisualNone-class config,clusterVisualNone-method execute,clusterVisualNone-method setup,clusterVisualNone-method setup<-,clusterVisualNone-method
Keywords: classes
Description: Class "clusterVisualNone", a placeholder for the goCluster visualization methods
URL: ../../../library/goCluster/html/clusterVisualNone-class.html

Entry: clusterclara
Aliases: clusterclara
Keywords: utilities
Description: Clusters a dataset with the clara function
URL: ../../../library/goCluster/html/clusterclara.html

Entry: clusterhclust
Aliases: clusterhclust
Keywords: utilities
Description: Clusters a dataset using hierarchical clustering
URL: ../../../library/goCluster/html/clusterhclust.html

Entry: clusterkmeans
Aliases: clusterkmeans
Keywords: utilities
Description: Clusters a dataset with the kmeans function
URL: ../../../library/goCluster/html/clusterkmeans.html

Entry: clusterpam
Aliases: clusterpam
Keywords: utilities
Description: Clusters a dataset with the pam function
URL: ../../../library/goCluster/html/clusterpam.html

Entry: config-methods
Aliases: config
Keywords: methods
Description: Interactively configure a goCluster-module
URL: ../../../library/goCluster/html/config-methods.html

Entry: convertlist
Aliases: convertlist convertontology convertevidence
Keywords: utilities
Description: Function to convert user input into a character vector
URL: ../../../library/goCluster/html/convertlist.html

Entry: evalClusterHyper
Aliases: evalClusterHyper evalAnnosetHyper
Keywords: utilities
Description: Evaluates a clustering result with regard to an enrichment of annotation terms in specific clusters.
URL: ../../../library/goCluster/html/evalClusterHyper.html

Entry: execute<--methods
Aliases: execute<-
Keywords: methods
Description: Configures and executes a goCluster-module
URL: ../../../library/goCluster/html/execute-assign-methods.html

Entry: execute-methods
Aliases: execute
Keywords: methods
Description: Executes a goCluster-module
URL: ../../../library/goCluster/html/execute-methods.html

Entry: getChildrenClasses
Aliases: getChildrenClasses
Keywords: utilities
Description: Get the children of an abstract class
URL: ../../../library/goCluster/html/getChildrenClasses.html

Entry: goCluster-class
Aliases: goCluster-class config,goCluster-method reset,goCluster-method run<-,goCluster-method run,goCluster-method setup<-,goCluster-method setup,goCluster-method
Keywords: classes
Description: Class "goCluster", a class for combining clustering results with functional annotation
URL: ../../../library/goCluster/html/goCluster-class.html

Entry: groupCount
Aliases: groupCount
Keywords: utilities
Description: Count the number of clusters
URL: ../../../library/goCluster/html/groupCount.html

Entry: prepareCHRannotation
Aliases: prepareCHRannotation
Keywords: utilities
Description: A function to prepare the gene localization for subsequent statistical analysis
URL: ../../../library/goCluster/html/prepareCHRannotation.html

Entry: prepareGOannotation
Aliases: prepareGOannotation
Keywords: utilities
Description: A function to prepare the gene ontology annotation for subsequent statistical analysis
URL: ../../../library/goCluster/html/prepareGOannotation.html

Entry: prepareHeatmap
Aliases: prepareHeatmap
Keywords: utilities
Description: A function to reformat a goCluster result for graphical representation
URL: ../../../library/goCluster/html/prepareHeatmap.html

Entry: reset-methods
Aliases: reset
Keywords: methods
Description: Reset a goCluster-module
URL: ../../../library/goCluster/html/reset-methods.html

Entry: goCluster FDR analysis
Aliases: randomizeTree mergeAnno selectAnnoStats
Keywords: utilities
Description: Select interesting annotation terms after FDR analysis
URL: ../../../library/goCluster/html/selectAnnoStats.html

Entry: selectChild
Aliases: selectChild
Keywords: utilities
Description: Choosing the child of an abstract class
URL: ../../../library/goCluster/html/selectChild.html

Entry: selectCore
Aliases: selectCore
Keywords: utilities
Description: A menu function
URL: ../../../library/goCluster/html/selectCore.html

Entry: selectDouble
Aliases: selectDouble
Keywords: utilities
Description: A menu for choosing a floating point number
URL: ../../../library/goCluster/html/selectDouble.html

Entry: selectNumber
Aliases: selectNumber
Keywords: utilities
Description: A menu for choosing an integer
URL: ../../../library/goCluster/html/selectNumber.html

Entry: selectOption
Aliases: selectOption
Keywords: utilities
Description: A menu for choosing an option
URL: ../../../library/goCluster/html/selectOption.html

Entry: selectStats
Aliases: selectStats
Keywords: utilities
Description: Selects relevant annotation terms
URL: ../../../library/goCluster/html/selectStats.html

Entry: selectStatsBonferroni
Aliases: selectStatsBonferroni
Keywords: utilities
Description: Performs Bonferroni correction and subsequently selects relevant annotation terms.
URL: ../../../library/goCluster/html/selectStatsBonferroni.html

Entry: selectTerms
Aliases: selectTerms
Keywords: utilities
Description: A function to select interesting annotation terms with the associated genes from a goCluster object
URL: ../../../library/goCluster/html/selectTerms.html

Entry: setup<--methods
Aliases: setup<-
Keywords: methods
Description: Configures a goCluster-object by assigning a list of parameters
URL: ../../../library/goCluster/html/setup-assign-methods.html

Entry: setup-methods
Aliases: setup
Keywords: methods
Description: Returns the setup of a goCluster-module
URL: ../../../library/goCluster/html/setup-methods.html
