# Statistical methods for the analysis of flow cytometry data

## Documentation for package ‘flowStats’ version 4.14.0

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

## Help Pages

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
ellipse | convert ellipse from cov/mu to points used to plot priors
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.
flowClust2Prior | Generate a prior specification based on a flowClust model This function generates a prior specification based on a flowClust fit object It can be passed to a second round of flowClust() with usePrior="yes" The prior could be estimated from a single sample, for example, and then used to speed up the convergence for other samples.
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.
mkPrior | Generate a flowClust prior specification
mkPrior-method | Generate a flowClust prior specification
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
plotPrior | Plots a flowClust prior over some 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"
SimulateMixture | Random Generation from a t Mixture Model with Box-Cox Transformation
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