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 |
fluidigmColData | Subset of fluidigm data |
fluidigmData | Subset of fluidigm data |
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 |
makeRsecFluidigmObject | Documentation of rsecFluidigm object |
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 | Documentation of rsecFluidigm object |
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 |