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 |