| 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 |