# Compare Clusterings for Single-Cell Sequencing

## Documentation for package ‘clusterExperiment’ version 2.14.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G I L M N O P R S T U W misc

## -- A --

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

## -- B --

bigPalette | Convert clusterLegend into useful formats
bubblePlot-method | Plot heatmap of cross-tabs of 2 clusterings

## -- C --

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

## -- D --

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

## -- E --

eraseMergeInfo | Merge clusters based on dendrogram
eraseMergeInfo-method | Merge clusters based on dendrogram

## -- F --

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

## -- G --

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

## -- I --

inputType | Helper methods for the ClusterFunction class
inputType-method | Helper methods for the ClusterFunction class
internalFunctionCheck | Class ClusterFunction

## -- L --

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

## -- M --

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

## -- N --

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

## -- O --

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

## -- P --

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

## -- R --

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

## -- S --

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

## -- T --

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

## -- U --

updateObject | Update old ClusterExperiment object to current class definition
updateObject-method | Update old ClusterExperiment object to current class definition

## -- W --

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

## -- misc --

[-method | Functions to subset ClusterExperiment Objects