# Clustering for Flow Cytometry

## Documentation for package ‘flowClust’ version 3.8.0

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

## Help Pages

flowClust-package | Clustering for Flow Cytometry
%in%-method | Robust Model-based Clustering for Flow Cytometry
%in%-method | Creating Filters and Filtering Flow Cytometry Data
box | Box-Cox Transformation
criterion | Various Functions for Retrieving Information from Clustering Results
criterion-method | Various Functions for Retrieving Information from Clustering Results
criterion<- | Various Functions for Retrieving Information from Clustering Results
criterion<--method | Various Functions for Retrieving Information from Clustering Results
density-method | Grid of Density Values for the Fitted t Mixture Model with Box-Cox Transformation
density.flowClust | Grid of Density Values for the Fitted t Mixture Model with Box-Cox Transformation
dmvt | Density of the Multivariate t Distribution with Box-Cox Tranformation
dmvtmix | Density of the Multivariate t Mixture Distribution with Box-Cox Tranformation
filter | Creating Filters and Filtering Flow Cytometry Data
filter-method | Creating Filters and Filtering Flow Cytometry Data
filter.flowFrame | Creating Filters and Filtering Flow Cytometry Data
flowClust | Robust Model-based Clustering for Flow Cytometry
flowClust-class | Robust Model-based Clustering for Flow Cytometry
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.
flowClustList | Robust Model-based Clustering for Flow Cytometry
flowClustList-class | Robust Model-based Clustering for Flow Cytometry
flowDens-class | Grid of Density Values for the Fitted t Mixture Model with Box-Cox Transformation
getEstimates | Various Functions for Retrieving Information from Clustering Results
hist-method | 1-D Density Plot (Histogram) of Clustering Results
hist.flowClust | 1-D Density Plot (Histogram) of Clustering Results
importance | Various Functions for Retrieving Information from Clustering Results
Map | Cluster Assignment Based on Clustering Results
Map-method | Cluster Assignment Based on Clustering Results
Map.flowClust | Cluster Assignment Based on Clustering Results
mkPrior | Generate a flowClust prior specification
mkPrior-method | Generate FlowClust prior Specifications
mkPrior-method | Generate a flowClust prior specification
mkPrior-methods | Generate FlowClust prior Specifications
peakMatch | Function to match peaks across samples
plot-method | Scatterplot of Clustering Results
plot-method | Scatterplot / 1-D Density Plot of Filtering (Clustering) Results
plot-method | Contour or Image Plot of Clustering Results
plot.flowClust | Scatterplot of Clustering Results
plot.flowDens | Contour or Image Plot of Clustering Results
plot.flowFrame | Scatterplot / 1-D Density Plot of Filtering (Clustering) Results
plot.flowFrame.tmixFilterResult | Scatterplot / 1-D Density Plot of Filtering (Clustering) Results
plot.tmixFilterResult | Scatterplot / 1-D Density Plot of Filtering (Clustering) Results
plotPrior | Plots a flowClust prior over some data.
posterior | Various Functions for Retrieving Information from Clustering Results
rbox | Reverse Box-Cox Transformation
rituximab | The Rituximab Dataset
ruleOutliers | Showing or Modifying the Rule used to Identify Outliers
ruleOutliers-method | Showing or Modifying the Rule used to Identify Outliers
ruleOutliers.flowClust | Showing or Modifying the Rule used to Identify Outliers
ruleOutliers<- | Showing or Modifying the Rule used to Identify Outliers
ruleOutliers<--method | Showing or Modifying the Rule used to Identify Outliers
show-method | Show Method for flowClust / tmixFilterResult Object
show-method | Show Method for tmixFilter Object
show.flowClust | Show Method for flowClust / tmixFilterResult Object
show.tmixFilter | Show Method for tmixFilter Object
show.tmixFilterResult | Show Method for flowClust / tmixFilterResult Object
SimulateMixture | Random Generation from a t Mixture Model with Box-Cox Transformation
split | Splitting Data Based on Clustering Results
split-method | Splitting Data Based on Clustering Results
split.flowClust | Splitting Data Based on Clustering Results
split.flowFrame | Splitting Data Based on Clustering Results
split.tmixFilterResult | Splitting Data Based on Clustering Results
Subset | Subsetting Data Based on Clustering Results
Subset-method | Subsetting Data Based on Clustering Results
Subset.flowClust | Subsetting Data Based on Clustering Results
Subset.flowFrame | Subsetting Data Based on Clustering Results
Subset.flowFrame.tmixFilterResult | Subsetting Data Based on Clustering Results
Subset.tmixFilterResult | Subsetting Data Based on Clustering Results
summary-method | Summary Method for flowClust Object
summary.flowClust | Summary Method for flowClust Object
summary.tmixFilterResult | Summary Method for flowClust Object
tmixFilter | Creating Filters and Filtering Flow Cytometry Data
tmixFilter-class | Creating Filters and Filtering Flow Cytometry Data
tmixFilterResult-class | Creating Filters and Filtering Flow Cytometry Data
tmixFilterResultList | Creating Filters and Filtering Flow Cytometry Data
tmixFilterResultList-class | Creating Filters and Filtering Flow Cytometry Data
uncertainty | Various Functions for Retrieving Information from Clustering Results
[-method | Robust Model-based Clustering for Flow Cytometry
[-method | Creating Filters and Filtering Flow Cytometry Data
[[-method | Creating Filters and Filtering Flow Cytometry Data