| 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 |