# Using Mass Cytometry for Differential Abundance Analyses

## Documentation for package ‘cydar’ version 1.4.0

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

## Help Pages

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