Analysis of clustering results in conjunction with annotation data.


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Documentation for package `goCluster' version 1.0.3

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B C D E G H M O P R S

-- B --

benomylsetup A test dataset for goCluster
benomylsetupsmall A test dataset for goCluster

-- C --

checkannotationpackage Check if an annotation package contains the specified environment.
checkchrannotation Check if an annotation package contains the specified environment.
checkData Checks if a variable contains data.
checkgoannotation Check if an annotation package contains the specified environment.
checkProtection A function to protect intermediate results from being overwritten
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.
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
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"
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
config,clusterAlgorithm-method Class "clusterAlgorithm"
config,clusterAlgorithmClara-method Class "clusterAlgorithmClara", provides partitioning around medoids of large datasets
config,clusterAlgorithmHclust-method Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.
config,clusterAlgorithmKmeans-method Class "clusterAlgorithmKmeans", provides kmeans clustering for goCluster.
config,clusterAlgorithmPam-method Class "clusterAlgorithmPam", provides partitioning around medoids for goCluster.
config,clusterAnnotation-method Class "clusterAnnotation", an abstract class that represents functions for annotating microarray datasets.
config,clusterAnnotationChromosome-abp-method Class "clusterAnnotationChromosome-abp", prepares the chromosome annotation for subsequent statistical analysis.
config,clusterAnnotationGO-abp-method Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.
config,clusterData-method Class "clusterData", a class for holding datasets that are going to be analysed with goCluster.
config,clusterModule-method Class "clusterModule" represents the base class for all goCluster objects
config,clusterSignif-method Class "clusterSignif"
config,clusterSignifBase-method Class "clusterSignifBase"
config,clusterSignifBonferroni-method Class "clusterSignifBonferroni"
config,clusterSignifFDR-method Class "clusterSignifFDR"
config,clusterStatistic-method Class "clusterStatistic" provides statistical analysis for goCluster
config,clusterStatisticHyper-method Class "clusterStatisticHyper" provides the hypergeometric distribution for the goCluster analysis.
config,clusterVisual-method Class "clusterVisual"
config,clusterVisualHclust-method Class "clusterVisualHclust" prepares a visualization for a dataset that has been clustered with hierarchical clustering.
config,clusterVisualHeatmap-method Class "clusterVisualHeatmap", prepares a goCluster analysis for visualization.
config,clusterVisualNone-method Class "clusterVisualNone", a placeholder for the goCluster visualization methods
config,goCluster-method Class "goCluster", a class for combining clustering results with functional annotation

-- D --

display Display a visualization module
display,clusterVisual-method Class "clusterVisual"
display,clusterVisualHclust-method Class "clusterVisualHclust" prepares a visualization for a dataset that has been clustered with hierarchical clustering.
display,clusterVisualHeatmap-method Class "clusterVisualHeatmap", prepares a goCluster analysis for visualization.
display,clusterVisualNone-method Class "clusterVisualNone", a placeholder for the goCluster visualization methods
display,goCluster-method Class "goCluster", a class for combining clustering results with functional annotation

-- E --

evalAnnosetHyper Evaluates a clustering result with regard to an enrichment of annotation terms in specific clusters.
evalClusterHyper Evaluates a clustering result with regard to an enrichment of annotation terms in specific clusters.
EVIDENCECODES Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.
execute Executes a goCluster-module
execute,clusterAlgorithm-method Class "clusterAlgorithm"
execute,clusterAlgorithmClara-method Class "clusterAlgorithmClara", provides partitioning around medoids of large datasets
execute,clusterAlgorithmHclust-method Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.
execute,clusterAlgorithmKmeans-method Class "clusterAlgorithmKmeans", provides kmeans clustering for goCluster.
execute,clusterAlgorithmPam-method Class "clusterAlgorithmPam", provides partitioning around medoids for goCluster.
execute,clusterAnnotation-method Class "clusterAnnotation", an abstract class that represents functions for annotating microarray datasets.
execute,clusterAnnotationChromosome-abp-method Class "clusterAnnotationChromosome-abp", prepares the chromosome annotation for subsequent statistical analysis.
execute,clusterAnnotationGO-abp-method Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.
execute,clusterData-method Class "clusterData", a class for holding datasets that are going to be analysed with goCluster.
execute,clusterModule-method Class "clusterModule" represents the base class for all goCluster objects
execute,clusterSignif-method Class "clusterSignif"
execute,clusterSignifBase-method Class "clusterSignifBase"
execute,clusterSignifBonferroni-method Class "clusterSignifBonferroni"
execute,clusterSignifFDR-method Class "clusterSignifFDR"
execute,clusterStatistic-method Class "clusterStatistic" provides statistical analysis for goCluster
execute,clusterStatisticHyper-method Class "clusterStatisticHyper" provides the hypergeometric distribution for the goCluster analysis.
execute,clusterVisual-method Class "clusterVisual"
execute,clusterVisualHclust-method Class "clusterVisualHclust" prepares a visualization for a dataset that has been clustered with hierarchical clustering.
execute,clusterVisualHeatmap-method Class "clusterVisualHeatmap", prepares a goCluster analysis for visualization.
execute,clusterVisualNone-method Class "clusterVisualNone", a placeholder for the goCluster visualization methods
execute<-,clusterModule-method Class "clusterModule" represents the base class for all goCluster objects

-- G --

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
goClusterTk Class "goCluster", a class for combining clustering results with functional annotation
groupCount Count the number of clusters

-- H --

HCLUSTDISTANCE Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.
HCLUSTMETHOD Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.

-- M --

mergeAnno Select interesting annotation terms after FDR analysis
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

-- O --

ONTOLOGIES Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.

-- P --

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
print,clusterAlgorithm-method Class "clusterAlgorithm"
print,clusterAlgorithmClara-method Class "clusterAlgorithmClara", provides partitioning around medoids of large datasets
print,clusterAlgorithmHclust-method Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.
print,clusterAlgorithmKmeans-method Class "clusterAlgorithmKmeans", provides kmeans clustering for goCluster.
print,clusterAlgorithmPam-method Class "clusterAlgorithmPam", provides partitioning around medoids for goCluster.
print,clusterAnnotation-method Class "clusterAnnotation", an abstract class that represents functions for annotating microarray datasets.
print,clusterAnnotationChromosome-abp-method Class "clusterAnnotationChromosome-abp", prepares the chromosome annotation for subsequent statistical analysis.
print,clusterAnnotationGO-abp-method Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.
print,clusterData-method Class "clusterData", a class for holding datasets that are going to be analysed with goCluster.
print,clusterSignif-method Class "clusterSignif"
print,clusterSignifBase-method Class "clusterSignifBase"
print,clusterSignifBonferroni-method Class "clusterSignifBonferroni"
print,clusterSignifFDR-method Class "clusterSignifFDR"
print,clusterStatistic-method Class "clusterStatistic" provides statistical analysis for goCluster
print,clusterStatisticHyper-method Class "clusterStatisticHyper" provides the hypergeometric distribution for the goCluster analysis.
print,clusterVisual-method Class "clusterVisual"
print,clusterVisualHclust-method Class "clusterVisualHclust" prepares a visualization for a dataset that has been clustered with hierarchical clustering.
print,clusterVisualHeatmap-method Class "clusterVisualHeatmap", prepares a goCluster analysis for visualization.
print,clusterVisualNone-method Class "clusterVisualNone", a placeholder for the goCluster visualization methods
print,goCluster-method Class "goCluster", a class for combining clustering results with functional annotation
printData Helper printing function

-- R --

randomizeTree Select interesting annotation terms after FDR analysis
reset Reset a goCluster-module
reset,clusterAlgorithm-method Class "clusterAlgorithm"
reset,clusterAlgorithmClara-method Class "clusterAlgorithmClara", provides partitioning around medoids of large datasets
reset,clusterAlgorithmHclust-method Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.
reset,clusterAlgorithmKmeans-method Class "clusterAlgorithmKmeans", provides kmeans clustering for goCluster.
reset,clusterAlgorithmPam-method Class "clusterAlgorithmPam", provides partitioning around medoids for goCluster.
reset,clusterAnnotation-method Class "clusterAnnotation", an abstract class that represents functions for annotating microarray datasets.
reset,clusterAnnotationChromosome-abp-method Class "clusterAnnotationChromosome-abp", prepares the chromosome annotation for subsequent statistical analysis.
reset,clusterAnnotationGO-abp-method Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.
reset,clusterData-method Class "clusterData", a class for holding datasets that are going to be analysed with goCluster.
reset,clusterModule-method Class "clusterModule" represents the base class for all goCluster objects
reset,clusterSignif-method Class "clusterSignif"
reset,clusterSignifBase-method Class "clusterSignifBase"
reset,clusterSignifBonferroni-method Class "clusterSignifBonferroni"
reset,clusterSignifFDR-method Class "clusterSignifFDR"
reset,clusterStatistic-method Class "clusterStatistic" provides statistical analysis for goCluster
reset,clusterStatisticHyper-method Class "clusterStatisticHyper" provides the hypergeometric distribution for the goCluster analysis.
reset,clusterVisual-method Class "clusterVisual"
reset,clusterVisualHclust-method Class "clusterVisualHclust" prepares a visualization for a dataset that has been clustered with hierarchical clustering.
reset,clusterVisualHeatmap-method Class "clusterVisualHeatmap", prepares a goCluster analysis for visualization.
reset,clusterVisualNone-method Class "clusterVisualNone", a placeholder for the goCluster visualization methods
reset,goCluster-method Class "goCluster", a class for combining clustering results with functional annotation
run,goCluster-method Class "goCluster", a class for combining clustering results with functional annotation
run<-,goCluster-method Class "goCluster", a class for combining clustering results with functional annotation

-- S --

selectAnnoStats Select interesting annotation terms after FDR analysis
selectChild Choosing the child of an abstract class
selectCore A menu function
selectCorePlain A menu function
selectCoreTk 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
selectOptions 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,clusterAlgorithm-method Class "clusterAlgorithm"
setup,clusterAlgorithmClara-method Class "clusterAlgorithmClara", provides partitioning around medoids of large datasets
setup,clusterAlgorithmHclust-method Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.
setup,clusterAlgorithmKmeans-method Class "clusterAlgorithmKmeans", provides kmeans clustering for goCluster.
setup,clusterAlgorithmPam-method Class "clusterAlgorithmPam", provides partitioning around medoids for goCluster.
setup,clusterAnnotation-method Class "clusterAnnotation", an abstract class that represents functions for annotating microarray datasets.
setup,clusterAnnotationChromosome-abp-method Class "clusterAnnotationChromosome-abp", prepares the chromosome annotation for subsequent statistical analysis.
setup,clusterAnnotationGO-abp-method Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.
setup,clusterData-method Class "clusterData", a class for holding datasets that are going to be analysed with goCluster.
setup,clusterModule-method Class "clusterModule" represents the base class for all goCluster objects
setup,clusterSignif-method Class "clusterSignif"
setup,clusterSignifBase-method Class "clusterSignifBase"
setup,clusterSignifBonferroni-method Class "clusterSignifBonferroni"
setup,clusterSignifFDR-method Class "clusterSignifFDR"
setup,clusterStatistic-method Class "clusterStatistic" provides statistical analysis for goCluster
setup,clusterStatisticHyper-method Class "clusterStatisticHyper" provides the hypergeometric distribution for the goCluster analysis.
setup,clusterVisual-method Class "clusterVisual"
setup,clusterVisualHclust-method Class "clusterVisualHclust" prepares a visualization for a dataset that has been clustered with hierarchical clustering.
setup,clusterVisualHeatmap-method Class "clusterVisualHeatmap", prepares a goCluster analysis for visualization.
setup,clusterVisualNone-method Class "clusterVisualNone", a placeholder for the goCluster visualization methods
setup,goCluster-method Class "goCluster", a class for combining clustering results with functional annotation
setup<-,clusterAlgorithm-method Class "clusterAlgorithm"
setup<-,clusterAlgorithmClara-method Class "clusterAlgorithmClara", provides partitioning around medoids of large datasets
setup<-,clusterAlgorithmHclust-method Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.
setup<-,clusterAlgorithmKmeans-method Class "clusterAlgorithmKmeans", provides kmeans clustering for goCluster.
setup<-,clusterAlgorithmPam-method Class "clusterAlgorithmPam", provides partitioning around medoids for goCluster.
setup<-,clusterAnnotation-method Class "clusterAnnotation", an abstract class that represents functions for annotating microarray datasets.
setup<-,clusterAnnotationChromosome-abp-method Class "clusterAnnotationChromosome-abp", prepares the chromosome annotation for subsequent statistical analysis.
setup<-,clusterAnnotationGO-abp-method Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.
setup<-,clusterData-method Class "clusterData", a class for holding datasets that are going to be analysed with goCluster.
setup<-,clusterModule-method Class "clusterModule" represents the base class for all goCluster objects
setup<-,clusterSignif-method Class "clusterSignif"
setup<-,clusterSignifBase-method Class "clusterSignifBase"
setup<-,clusterSignifBonferroni-method Class "clusterSignifBonferroni"
setup<-,clusterSignifFDR-method Class "clusterSignifFDR"
setup<-,clusterStatistic-method Class "clusterStatistic" provides statistical analysis for goCluster
setup<-,clusterStatisticHyper-method Class "clusterStatisticHyper" provides the hypergeometric distribution for the goCluster analysis.
setup<-,clusterVisual-method Class "clusterVisual"
setup<-,clusterVisualHclust-method Class "clusterVisualHclust" prepares a visualization for a dataset that has been clustered with hierarchical clustering.
setup<-,clusterVisualHeatmap-method Class "clusterVisualHeatmap", prepares a goCluster analysis for visualization.
setup<-,clusterVisualNone-method Class "clusterVisualNone", a placeholder for the goCluster visualization methods
setup<-,goCluster-method Class "goCluster", a class for combining clustering results with functional annotation