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. |
clusterAnnotationLookup-class |
Class "clusterAnnotationLookup", provides LocusLink -> GO annotation information via an external lookup table. |
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,clusterAnnotationLookup-method |
Class "clusterAnnotationLookup", provides LocusLink -> GO annotation information via an external lookup table. |
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 |
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,clusterAnnotationLookup-method |
Class "clusterAnnotationLookup", provides LocusLink -> GO annotation information via an external lookup table. |
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 |
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,clusterAnnotationLookup-method |
Class "clusterAnnotationLookup", provides LocusLink -> GO annotation information via an external lookup table. |
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 |
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,clusterAnnotationLookup-method |
Class "clusterAnnotationLookup", provides LocusLink -> GO annotation information via an external lookup table. |
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 |
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,clusterAnnotationLookup-method |
Class "clusterAnnotationLookup", provides LocusLink -> GO annotation information via an external lookup table. |
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<-,clusterAnnotationLookup-method |
Class "clusterAnnotationLookup", provides LocusLink -> GO annotation information via an external lookup table. |
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 |