# A framework for two-class classification problems, with applications to differential variability and differential distribution testing

## Documentation for package ‘ClassifyR’ version 1.12.2

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

## Help Pages

actualClasses | Container for Storing Classification Results
actualClasses-method | Container for Storing Classification Results
bartlettSelection | Selection of Differential Variability with Bartlett Statistic
bartlettSelection-method | Selection of Differential Variability with Bartlett Statistic
calcPerformance | Add Performance Calculations to a ClassifyResult object
calcPerformance-method | Add Performance Calculations to a ClassifyResult object
classifyInterface | Interface for PoiClaClu Package's Classify Function
ClassifyResult | Container for Storing Classification Results
ClassifyResult-class | Container for Storing Classification Results
ClassifyResult-method | Container for Storing Classification Results
distribution | Get Frequencies of Feature Selection and Sample Errors
distribution-method | Get Frequencies of Feature Selection and Sample Errors
DMDselection | Selection of Differential Distributions with Differences in Means or Medians and a Deviation Measure
DMDselection-method | Selection of Differential Distributions with Differences in Means or Medians and a Deviation Measure
edgeRselection | Feature Selection Based on Differential Expression for RNA-seq
edgeRselection-method | Feature Selection Based on Differential Expression for RNA-seq
features | Container for Storing Classification Results
features-method | Container for Storing Classification Results
fisherDiscriminant | Classification Using Fisher's LDA
fisherDiscriminant-method | Classification Using Fisher's LDA
functionOrList | Union of Functions and List of Functions
functionOrList-class | Union of Functions and List of Functions
getLocationsAndScales | Calculate Location and Scale
getLocationsAndScales-method | Calculate Location and Scale
KolmogorovSmirnovSelection | Selection of Differential Distributions with Kolmogorov-Smirnov Distance
KolmogorovSmirnovSelection-method | Selection of Differential Distributions with Kolmogorov-Smirnov Distance
KullbackLeiblerSelection | Selection of Differential Distributions with Kullback Leibler Distance
KullbackLeiblerSelection-method | Selection of Differential Distributions with Kullback Leibler Distance
leveneSelection | Selection of Differential Variability with Levene Statistic
leveneSelection-method | Selection of Differential Variability with Levene Statistic
likelihoodRatioSelection | Selection of Differential Distributions with Likelihood Ratio Statistic
likelihoodRatioSelection-method | Selection of Differential Distributions with Likelihood Ratio Statistic
limmaSelection | Selection of Differentially Expressed Features
limmaSelection-method | Selection of Differentially Expressed Features
medianDifferenceSelection | Selection of Differential Expression by Comparing Differences in Medians of Groups
medianDifferenceSelection-method | Selection of Differential Expression by Comparing Differences in Medians of Groups
mixmodels | Selection of Differential Distributions with Mixtures of Normals
mixModelsTest | Selection of Differential Distributions with Mixtures of Normals
mixModelsTest-method | Selection of Differential Distributions with Mixtures of Normals
mixModelsTrain | Selection of Differential Distributions with Mixtures of Normals
mixModelsTrain-method | Selection of Differential Distributions with Mixtures of Normals
naiveBayesKernel | Classification Using A Bayes Classifier with Kernel Density Estimates
naiveBayesKernel-method | Classification Using A Bayes Classifier with Kernel Density Estimates
nearestShrunkenCentroidPredictInterface | Interface for 'pamr.predict' Function from 'pamr' CRAN Package
nearestShrunkenCentroidPredictInterface-method | Interface for 'pamr.predict' Function from 'pamr' CRAN Package
nearestShrunkenCentroidSelectionInterface | Interface for 'pamr.listgenes' Function from 'pamr' CRAN Package
nearestShrunkenCentroidSelectionInterface-method | Interface for 'pamr.listgenes' Function from 'pamr' CRAN Package
nearestShrunkenCentroidTrainInterface | Interface for 'pamr.train' Function from 'pamr' CRAN Package
nearestShrunkenCentroidTrainInterface-method | Interface for 'pamr.train' Function from 'pamr' CRAN Package
pamrtrained | Trained pamr Object
pamrtrained-class | Trained pamr Object
performance | Container for Storing Classification Results
performance-method | Container for Storing Classification Results
performancePlot | Plot Performance Measures for Various Classifications
performancePlot-method | Plot Performance Measures for Various Classifications
plotFeatureClasses | Plot Density and Scatterplot for Genes By Class
plotFeatureClasses-method | Plot Density and Scatterplot for Genes By Class
predictions | Container for Storing Classification Results
predictions-method | Container for Storing Classification Results
PredictParams | Parameters for Classifier Prediction
PredictParams-class | Parameters for Classifier Prediction
PredictParams-method | Parameters for Classifier Prediction
previousSelection | Automated Selection of Previously Selected Features
previousSelection-method | Automated Selection of Previously Selected Features
rankingPlot | Plot Pair-wise Overlap of Ranked Features
rankingPlot-method | Plot Pair-wise Overlap of Ranked Features
ResubstituteParams | Parameters for Resubstitution Error Calculation
ResubstituteParams-class | Parameters for Resubstitution Error Calculation
ResubstituteParams-method | Parameters for Resubstitution Error Calculation
ROCplot | Plot Receiver Operating Curve Graphs for Classification Results
ROCplot-method | Plot Receiver Operating Curve Graphs for Classification Results
runTest | Perform a Single Classification
runTest-method | Perform a Single Classification
runTests | Reproducibly Run Various Kinds of Cross-Validation
runTests-method | Reproducibly Run Various Kinds of Cross-Validation
samplesMetricMap | Plot a Grid of Sample Error Rates or Accuracies
samplesMetricMap-method | Plot a Grid of Sample Error Rates or Accuracies
selectionPlot | Plot Pair-wise Overlap or Selection Size Distribution of Selected Features
selectionPlot-method | Plot Pair-wise Overlap or Selection Size Distribution of Selected Features
SelectParams | Parameters for Feature Selection
SelectParams-class | Parameters for Feature Selection
SelectParams-method | Parameters for Feature Selection
SelectResult | Container for Storing Feature Selection Results
SelectResult-class | Container for Storing Feature Selection Results
SelectResult-method | Container for Storing Feature Selection Results
show-method | Container for Storing Classification Results
show-method | Container for Storing Feature Selection Results
subtractFromLocation | Subtract All Feature Measurements from Location
subtractFromLocation-method | Subtract All Feature Measurements from Location
totalPredictions | Container for Storing Classification Results
totalPredictions-method | Container for Storing Classification Results
TrainParams | Parameters for Classifier Training
TrainParams-class | Parameters for Classifier Training
TrainParams-method | Parameters for Classifier Training
TransformParams | Parameters for Data Transformation
TransformParams-class | Parameters for Data Transformation
TransformParams-method | Parameters for Data Transformation
tunedParameters | Container for Storing Classification Results
tunedParameters-method | Container for Storing Classification Results