![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
A B C D E F G I L M N O P R S T U W misc
| addClusterings | Add clusterings to ClusterExperiment object |
| addClusterings-method | Add clusterings to ClusterExperiment object |
| addToColData | Helper methods for the ClusterExperiment class |
| addToColData-method | Helper methods for the ClusterExperiment class |
| algorithmType | Helper methods for the ClusterFunction class |
| algorithmType-method | Helper methods for the ClusterFunction class |
| assignUnassigned | Assign unassigned samples to nearest cluster |
| assignUnassigned-method | Assign unassigned samples to nearest cluster |
| bigPalette | Convert clusterLegend into useful formats |
| bubblePlot-method | Plot heatmap of cross-tabs of 2 clusterings |
| checkDendrogram | Accessing and manipulating the dendrograms |
| checkDendrogram-method | Accessing and manipulating the dendrograms |
| clusterContrasts | Create contrasts for testing DE of a cluster |
| clusterContrasts-method | Create contrasts for testing DE of a cluster |
| clusterDendrogram | Accessing and manipulating the dendrograms |
| clusterDendrogram-method | Accessing and manipulating the dendrograms |
| ClusterExperiment | Class ClusterExperiment |
| ClusterExperiment-class | Class ClusterExperiment |
| clusterExperiment-deprecated | Deprecated functions in package 'clusterExperiment' |
| ClusterExperiment-method | Class ClusterExperiment |
| ClusterExperiment-methods | Helper methods for the ClusterExperiment class |
| ClusterFunction | Class ClusterFunction |
| ClusterFunction-class | Class ClusterFunction |
| ClusterFunction-method | Class ClusterFunction |
| ClusterFunction-methods | Helper methods for the ClusterFunction class |
| clusteringInfo | Helper methods for the ClusterExperiment class |
| clusteringInfo-method | Helper methods for the ClusterExperiment class |
| clusterLabels | Helper methods for the ClusterExperiment class |
| clusterLabels-method | Helper methods for the ClusterExperiment class |
| clusterLabels<- | Helper methods for the ClusterExperiment class |
| clusterLabels<--method | Helper methods for the ClusterExperiment class |
| clusterLegend | Helper methods for the ClusterExperiment class |
| clusterLegend-method | Helper methods for the ClusterExperiment class |
| clusterLegend<- | Helper methods for the ClusterExperiment class |
| clusterLegend<--method | Helper methods for the ClusterExperiment class |
| clusterMany | Create a matrix of clustering across values of parameters |
| clusterMany-method | Create a matrix of clustering across values of parameters |
| clusterMatrix | Helper methods for the ClusterExperiment class |
| clusterMatrix-method | Helper methods for the ClusterExperiment class |
| clusterMatrixColors | Helper methods for the ClusterExperiment class |
| clusterMatrixColors-method | Helper methods for the ClusterExperiment class |
| clusterMatrixNamed | Helper methods for the ClusterExperiment class |
| clusterMatrixNamed-method | Helper methods for the ClusterExperiment class |
| clusterSingle | General wrapper method to cluster the data |
| clusterSingle-method | General wrapper method to cluster the data |
| clusterTypes | Helper methods for the ClusterExperiment class |
| clusterTypes-method | Helper methods for the ClusterExperiment class |
| clusterTypes<- | Helper methods for the ClusterExperiment class |
| clusterTypes<--method | Helper methods for the ClusterExperiment class |
| coClustering | Helper methods for the ClusterExperiment class |
| coClustering-method | Helper methods for the ClusterExperiment class |
| coClustering<- | Helper methods for the ClusterExperiment class |
| coClustering<--method | Helper methods for the ClusterExperiment class |
| colDataClusters | Helper methods for the ClusterExperiment class |
| colDataClusters-method | Helper methods for the ClusterExperiment class |
| combineMany | Deprecated functions in package 'clusterExperiment' |
| combineMany-method | Deprecated functions in package 'clusterExperiment' |
| convertClusterLegend | Convert clusterLegend into useful formats |
| convertClusterLegend-method | Convert clusterLegend into useful formats |
| convertToDendrogram | Accessing and manipulating the dendrograms |
| convertToDendrogram-method | Accessing and manipulating the dendrograms |
| defaultNDims | Return matrix from ClusterExperiment with reduced dimensions |
| defaultNDims-method | Return matrix from ClusterExperiment with reduced dimensions |
| dendroClusterIndex | Helper methods for the ClusterExperiment class |
| dendroClusterIndex-method | Helper methods for the ClusterExperiment class |
| eraseMergeInfo | Merge clusters based on dendrogram |
| eraseMergeInfo-method | Merge clusters based on dendrogram |
| filterData | Return matrix from ClusterExperiment with reduced dimensions |
| filterData-method | Return matrix from ClusterExperiment with reduced dimensions |
| filterNames | Return matrix from ClusterExperiment with reduced dimensions |
| filterNames-method | Return matrix from ClusterExperiment with reduced dimensions |
| getBestFeatures | Function for finding best features associated with clusters |
| getBestFeatures-method | Function for finding best features associated with clusters |
| getBuiltInFunction | Built in ClusterFunction options |
| getBuiltInFunction-method | Built in ClusterFunction options |
| getClusterIndex | getClusterIndex |
| getClusterIndex-method | getClusterIndex |
| getClusterManyParams | Get parameter values of clusterMany clusters |
| getClusterManyParams-method | Get parameter values of clusterMany clusters |
| getMergeCorrespond | Merge clusters based on dendrogram |
| getMergeCorrespond-method | Merge clusters based on dendrogram |
| getPostProcessingArgs | Cluster distance matrix from subsampling |
| getPostProcessingArgs-method | Cluster distance matrix from subsampling |
| getReducedData | Return matrix from ClusterExperiment with reduced dimensions |
| getReducedData-method | Return matrix from ClusterExperiment with reduced dimensions |
| getSingleClusterIndex | getClusterIndex |
| getSingleClusterIndex-method | getClusterIndex |
| inputType | Helper methods for the ClusterFunction class |
| inputType-method | Helper methods for the ClusterFunction class |
| internalFunctionCheck | Class ClusterFunction |
| listBuiltInFilterStats | Return matrix from ClusterExperiment with reduced dimensions |
| listBuiltInFunctions | Built in ClusterFunction options |
| listBuiltInReducedDims | Return matrix from ClusterExperiment with reduced dimensions |
| listBuiltInType01 | Built in ClusterFunction options |
| listBuiltInTypeK | Built in ClusterFunction options |
| mainClustering | Cluster distance matrix from subsampling |
| mainClustering-method | Cluster distance matrix from subsampling |
| makeBlankData | Convert clusterLegend into useful formats |
| makeConsensus | Find sets of samples that stay together across clusterings |
| makeConsensus-method | Find sets of samples that stay together across clusterings |
| makeDendrogram | Make hierarchy of set of clusters |
| makeDendrogram-method | Make hierarchy of set of clusters |
| makeFilterStats | Return matrix from ClusterExperiment with reduced dimensions |
| makeFilterStats-method | Return matrix from ClusterExperiment with reduced dimensions |
| makeReducedDims | Return matrix from ClusterExperiment with reduced dimensions |
| makeReducedDims-method | Return matrix from ClusterExperiment with reduced dimensions |
| massivePalette | Convert clusterLegend into useful formats |
| mergeClusterIndex | Merge clusters based on dendrogram |
| mergeClusterIndex-method | Merge clusters based on dendrogram |
| mergeClusters | Merge clusters based on dendrogram |
| mergeClusters-method | Merge clusters based on dendrogram |
| mergeCutoff | Merge clusters based on dendrogram |
| mergeCutoff-method | Merge clusters based on dendrogram |
| mergeMethod | Merge clusters based on dendrogram |
| mergeMethod-method | Merge clusters based on dendrogram |
| nClusterings | Helper methods for the ClusterExperiment class |
| nClusterings-method | Helper methods for the ClusterExperiment class |
| nClusters | Helper methods for the ClusterExperiment class |
| nClusters-method | Helper methods for the ClusterExperiment class |
| nFeatures | Helper methods for the ClusterExperiment class |
| nFeatures-method | Helper methods for the ClusterExperiment class |
| nInternalNodes | Accessing and manipulating the dendrograms |
| nInternalNodes-method | Accessing and manipulating the dendrograms |
| nNodes | Accessing and manipulating the dendrograms |
| nNodes-method | Accessing and manipulating the dendrograms |
| nodeIds | Accessing and manipulating the dendrograms |
| nodeIds-method | Accessing and manipulating the dendrograms |
| nodeLabels | Accessing and manipulating the dendrograms |
| nodeLabels-method | Accessing and manipulating the dendrograms |
| nodeLabels<- | Accessing and manipulating the dendrograms |
| nodeLabels<--method | Accessing and manipulating the dendrograms |
| nodeMergeInfo | Merge clusters based on dendrogram |
| nodeMergeInfo-method | Merge clusters based on dendrogram |
| nSamples | Helper methods for the ClusterExperiment class |
| nSamples-method | Helper methods for the ClusterExperiment class |
| nTips | Accessing and manipulating the dendrograms |
| nTips-method | Accessing and manipulating the dendrograms |
| numericalAsCharacter | Convert numeric values to character that sort correctly |
| orderSamples | Helper methods for the ClusterExperiment class |
| orderSamples-method | Helper methods for the ClusterExperiment class |
| orderSamples<- | Helper methods for the ClusterExperiment class |
| orderSamples<--method | Helper methods for the ClusterExperiment class |
| plotBarplot | Barplot of 1 or 2 clusterings |
| plotBarplot-method | Barplot of 1 or 2 clusterings |
| plotClusterLegend | Convert clusterLegend into useful formats |
| plotClusterLegend-method | Convert clusterLegend into useful formats |
| plotClusters | Visualize cluster assignments across multiple clusterings |
| plotClusters-method | Visualize cluster assignments across multiple clusterings |
| plotClustersTable | Plot heatmap of cross-tabs of 2 clusterings |
| plotClustersTable-method | Plot heatmap of cross-tabs of 2 clusterings |
| plotClustersWorkflow | A plot of clusterings specific for clusterMany and workflow visualization |
| plotClustersWorkflow-method | A plot of clusterings specific for clusterMany and workflow visualization |
| plotCoClustering | Heatmap for showing clustering results and more |
| plotCoClustering-method | Heatmap for showing clustering results and more |
| plotContrastHeatmap | Plot heatmaps showing significant genes per contrast |
| plotContrastHeatmap-method | Plot heatmaps showing significant genes per contrast |
| plotDendrogram | Plot dendrogram of ClusterExperiment object |
| plotDendrogram-method | Plot dendrogram of ClusterExperiment object |
| plotFeatureBoxplot | Plot boxplot of feature values by cluster |
| plotFeatureBoxplot-method | Plot boxplot of feature values by cluster |
| plotFeatureScatter | Plot scatter plot of feature values colored by cluster |
| plotFeatureScatter-method | Plot scatter plot of feature values colored by cluster |
| plotHeatmap | Heatmap for showing clustering results and more |
| plotHeatmap-method | Heatmap for showing clustering results and more |
| plotReducedDims | Plot 2-dimensionsal representation with clusters |
| plotReducedDims-method | Plot 2-dimensionsal representation with clusters |
| plottingFunctions | Convert clusterLegend into useful formats |
| primaryCluster | Helper methods for the ClusterExperiment class |
| primaryCluster-method | Helper methods for the ClusterExperiment class |
| primaryClusterIndex | Helper methods for the ClusterExperiment class |
| primaryClusterIndex-method | Helper methods for the ClusterExperiment class |
| primaryClusterIndex<- | Helper methods for the ClusterExperiment class |
| primaryClusterIndex<--method | Helper methods for the ClusterExperiment class |
| primaryClusterLabel | Helper methods for the ClusterExperiment class |
| primaryClusterLabel-method | Helper methods for the ClusterExperiment class |
| primaryClusterNamed | Helper methods for the ClusterExperiment class |
| primaryClusterNamed-method | Helper methods for the ClusterExperiment class |
| primaryClusterType | Helper methods for the ClusterExperiment class |
| primaryClusterType-method | Helper methods for the ClusterExperiment class |
| recolorClusters | Change assigned names or colors of clusters |
| recolorClusters-method | Change assigned names or colors of clusters |
| reduceFunctions | Return matrix from ClusterExperiment with reduced dimensions |
| removeClusterings | Add clusterings to ClusterExperiment object |
| removeClusterings-method | Functions to subset ClusterExperiment Objects |
| removeClusters | Functions to subset ClusterExperiment Objects |
| removeClusters-method | Functions to subset ClusterExperiment Objects |
| removeUnassigned | Assign unassigned samples to nearest cluster |
| removeUnassigned-method | Assign unassigned samples to nearest cluster |
| renameClusters | Change assigned names or colors of clusters |
| renameClusters-method | Change assigned names or colors of clusters |
| requiredArgs | Helper methods for the ClusterFunction class |
| requiredArgs-method | Helper methods for the ClusterFunction class |
| RSEC | Resampling-based Sequential Ensemble Clustering |
| RSEC-method | Resampling-based Sequential Ensemble Clustering |
| RSEC-methods | Resampling-based Sequential Ensemble Clustering |
| rsecFluidigm | RSEC run for vignette |
| sampleDendrogram | Accessing and manipulating the dendrograms |
| sampleDendrogram-method | Accessing and manipulating the dendrograms |
| search_pairs | Search pairs of samples that co-cluster across subsamples |
| seqCluster | Program for sequentially clustering, removing cluster, and starting again. |
| seqPal1 | Convert clusterLegend into useful formats |
| seqPal2 | Convert clusterLegend into useful formats |
| seqPal3 | Convert clusterLegend into useful formats |
| seqPal4 | Convert clusterLegend into useful formats |
| seqPal5 | Convert clusterLegend into useful formats |
| setBreaks | Convert clusterLegend into useful formats |
| setToCurrent | Methods for workflow clusters |
| setToCurrent-method | Methods for workflow clusters |
| setToFinal | Methods for workflow clusters |
| setToFinal-method | Methods for workflow clusters |
| show | Helper methods for the ClusterExperiment class |
| show-method | Helper methods for the ClusterExperiment class |
| showHeatmapPalettes | Convert clusterLegend into useful formats |
| showPalette | Convert clusterLegend into useful formats |
| simCount | Simulated data for running examples |
| simData | Simulated data for running examples |
| subsampleClustering | Cluster subsamples of the data |
| subsampleClustering-method | Cluster subsamples of the data |
| subset | Functions to subset ClusterExperiment Objects |
| subsetByCluster | Functions to subset ClusterExperiment Objects |
| subsetByCluster-method | Functions to subset ClusterExperiment Objects |
| tableClusters | Plot heatmap of cross-tabs of 2 clusterings |
| tableClusters-method | Plot heatmap of cross-tabs of 2 clusterings |
| transformation | Helper methods for the ClusterExperiment class |
| transformation-method | Helper methods for the ClusterExperiment class |
| transformation<- | Helper methods for the ClusterExperiment class |
| transformation<--method | Helper methods for the ClusterExperiment class |
| transformData | Transform the original data in a ClusterExperiment object |
| transformData-method | Transform the original data in a ClusterExperiment object |
| trueCluster | Simulated data for running examples |
| updateObject | Update old ClusterExperiment object to current class definition |
| updateObject-method | Update old ClusterExperiment object to current class definition |
| workflowClusterDetails | Methods for workflow clusters |
| workflowClusterDetails-method | Methods for workflow clusters |
| workflowClusters | Methods for workflow clusters |
| workflowClusters-method | Methods for workflow clusters |
| workflowClusterTable | Methods for workflow clusters |
| workflowClusterTable-method | Methods for workflow clusters |
| [-method | Functions to subset ClusterExperiment Objects |