Statistical methods for the analysis of flow cytometry data


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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