Using Mass Cytometry for Differential Abundance Analyses

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Documentation for package ‘cydar’ version 1.4.0

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c-method Subsetting and combining CyData
cbind-method Subsetting and combining CyData
cellAssignments CyData getters and setters
cellAssignments-method CyData getters and setters
cellAssignments<- CyData getters and setters
cellAssignments<--method CyData getters and setters
cellData CyData getters and setters
cellData-method CyData getters and setters
cellData<- CyData getters and setters
cellData<--method CyData getters and setters
cellIntensities CyData getters and setters
cellIntensities-method CyData getters and setters
cellIntensities<- CyData getters and setters
cellIntensities<--method CyData getters and setters
countCells Count cells in high-dimensional space
CyData CyData class and methods
CyData-class CyData class and methods
diffIntDistr Compute differences in intensity distributions
dnaGate Gate events based on DNA channels
expandRadius Expand the hypersphere radius
findFirstSphere Identifies the first non-redundant hyperspheres
intensities CyData getters and setters
intensities-method CyData getters and setters
intensities<- CyData getters and setters
intensities<--method CyData getters and setters
intensityRanges Define intensity ranges
interpretSpheres Interactive interpretation of hyperspheres
labelSpheres Label unannotated hyperspheres
markerData CyData getters and setters
markerData-method CyData getters and setters
markerData<- CyData getters and setters
markerData<--method CyData getters and setters
markernames CyData getters and setters
markernames-method CyData getters and setters
markernames<- CyData getters and setters
markernames<--method CyData getters and setters
medIntensities Compute median marker intensities
multiIntHist multiIntHist
ncells CyData getters and setters
ncells-method CyData getters and setters
neighborDistances Compute distances to neighbors
nmarkers CyData getters and setters
nmarkers-method CyData getters and setters
normalizeBatch Normalize intensities across batches
outlierGate Create an outlier gate
packIndices Pack or unpack indices
pickBestMarkers Pick best markers
plotCellIntensity Plot cell or hypersphere data
plotCellLogFC Plot cell or hypersphere data
poolCells Pool cells for pre-processing
prepareCellData Prepare mass cytometry data
rbind-method Subsetting and combining CyData
recountCells Recount cells in each group
sampleNames CyData getters and setters
sampleNames-method CyData getters and setters
sampleNames<- CyData getters and setters
sampleNames<--method CyData getters and setters
show-method CyData class and methods
spatialFDR Compute the spatial FDR
subset-method Subsetting and combining CyData
unpackIndices Pack or unpack indices
[-method Subsetting and combining CyData
[<--method Subsetting and combining CyData