Statistical methods for the analysis of flow cytometry data

Documentation for package ‘flowStats’ version 4.4.0

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flowStats-package	Statistical methods for flow cytometry data analysis
%in%-method	Class "curv1Filter"
%in%-method	Class "curv2Filter"
%in%-method	Automated gating of elliptical cell populations in 2D.
%in%-method	Class "norm2Filter"
%in%-method	Find most likely separation between positive and negative populations in 1D
addName-method	These methods are copied from flowViz to eliminate its dependency on curv1Filter and curv2Filter
autoGate	Automated gating of single populations in 2D
BackGating	Sample backgating results
binByRef	Bin a test data set using bins previously created by probability binning a control dataset
calcPBChiSquare	Probability binning metirc for comparing the probability binned datasets
calcPearsonChi	Pearsons chi-square statistic for comparing the probability binned datasets
curv1Filter	Class "curv1Filter"
curv1Filter-class	Class "curv1Filter"
curv2Filter	Class "curv2Filter"
curv2Filter-class	Class "curv2Filter"
curvPeaks	Parse curv1Filter output
density1d	Find most likely separation between positive and negative populations in 1D
fdPar	The version of fdPar from fda 2.4.0 because the new API changes the output. (specifically res$fd$coefs) and thus breaks the landmarkreg call.
flowStats	Statistical methods for flow cytometry data analysis
gate_singlet	Creates a singlet polygon gate using the prediction bands from a robust linear model
gaussNorm	Per-channel normalization based on landmark registration
gpaSet	Multi-dimensional normalization of flow cytometry data
idFeatures	(Internal use only) Identify features of flow cytometry data using backgating
idFeaturesByBackgating	(Internal use only) Identify features of flow cytometry data using backgating
iProcrustes	Procrustes analysis. Using singular value decomposition (SVD) to determine a linear transformation to align the points in X to the points in a reference matrix Y.
ITN	Sample flow cytometry data
landmarkMatrix	Compute and cluster high density regions in 1D
lymphFilter	Automated gating of elliptical cell populations in 2D.
lymphFilter-class	Automated gating of elliptical cell populations in 2D.
lymphGate	Automated gating of elliptical cell populations in 2D.
norm2Filter	Class "norm2Filter"
norm2Filter-class	Class "norm2Filter"
normalize	normalize a GatingSet imported with flowWorkspace, using sequential normalization on the manual gates in the GatingHierarchy.
normalize-method	normalize a GatingSet imported with flowWorkspace, using sequential normalization on the manual gates in the GatingHierarchy.
normalize-methods	normalize a GatingSet imported with flowWorkspace, using sequential normalization on the manual gates in the GatingHierarchy.
normQA	Normalization quality assessment
oneDGate	Find most likely separation between positive and negative populations in 1D
overton_like	Overton-like subtraction of densities.
plotBins	Plots the probability bins overlaid with flowFrame data
proBin	Probability binning - a metric for evaluating multivariate differences
quadrantGate	Automated quad gating
rangeFilter	Find most likely separation between positive and negative populations in 1D
rangeFilter-class	Find most likely separation between positive and negative populations in 1D
rangeGate	Find most likely separation between positive and negative populations in 1D
show-method	Class "curv1Filter"
show-method	Class "curv2Filter"
show-method	Class "norm2Filter"
singletGate	Creates a singlet polygon gate using the prediction bands from a robust linear model
spillover	Compute a spillover matrix from a flowSet
spillover-flowSet	Compute a spillover matrix from a flowSet
spillover-method	Compute a spillover matrix from a flowSet
spillover_match	Construct a 'flowSet' for use with 'spillover' by matching channel names to compensation control filenames
spillover_match-flowSet	Construct a 'flowSet' for use with 'spillover' by matching channel names to compensation control filenames
spillover_match-method	Construct a 'flowSet' for use with 'spillover' by matching channel names to compensation control filenames
spillover_ng	Compute a spillover matrix from a 'flowSet', simplified API
spillover_ng-flowSet	Compute a spillover matrix from a 'flowSet', simplified API
spillover_ng-method	Compute a spillover matrix from a 'flowSet', simplified API
summarizeFilter-method	Class "curv1Filter"
summarizeFilter-method	Class "curv2Filter"
warpSet	Normalization based on landmark registration
warpSet.cytoset	Normalization based on landmark registration
warpSetGS	Normalization based on landmark registration
warpSetNCDF	Normalization based on landmark registration
warpSetNCDFLowMem	Normalization based on landmark registration