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

## Documentation for package ‘ClassifyR’ version 3.0.3

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

## Help Pages

A B C D E F G H I K L M N P R S T misc

## -- A --

actualOutcomes | Container for Storing Classification Results
actualOutcomes-method | Container for Storing Classification Results
allFeatureNames | Container for Storing Classification Results
allFeatureNames-method | Container for Storing Classification Results
asthma | Asthma RNA Abundance and Patient Classes

## -- B --

bartlettRanking | Ranking of Differential Variability with Bartlett Statistic
bartlettRanking-method | Ranking of Differential Variability with Bartlett Statistic

## -- C --

calcCVperformance | Add Performance Calculations to a ClassifyResult Object or Calculate for a Pair of Factor Vectors
calcCVperformance-method | Add Performance Calculations to a ClassifyResult Object or Calculate for a Pair of Factor Vectors
calcExternalPerformance | Add Performance Calculations to a ClassifyResult Object or Calculate for a Pair of Factor Vectors
calcExternalPerformance-method | Add Performance Calculations to a ClassifyResult Object or Calculate for a Pair of Factor Vectors
calcPerformance | Add Performance Calculations to a ClassifyResult Object or Calculate for a Pair of Factor Vectors
characterOrDataFrame | Union of a Character and a DataFrame
characterOrDataFrame-class | Union of a Character and a DataFrame
chosenFeatureNames | Container for Storing Classification Results
chosenFeatureNames-method | Container for Storing Classification Results
classes | Asthma RNA Abundance and Patient Classes
classifyInterface | An Interface for PoiClaClu Package's Classify Function
classifyInterface-method | An 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
coxnetInterface | An Interface for glmnet Package's coxnet Function
coxnetPredictInterface | An Interface for glmnet Package's coxnet Function
coxnetPredictInterface-method | An Interface for glmnet Package's coxnet Function
coxnetTrainInterface | An Interface for glmnet Package's coxnet Function
coxnetTrainInterface-method | An Interface for glmnet Package's coxnet Function
coxph | Trained coxph Object
coxph-class | Trained coxph Object
coxphInterface | An Interface for survival Package's coxph Function
coxphInterface-method | An Interface for survival Package's coxph Function
coxphPredictInterface | An Interface for survival Package's coxph Function
coxphPredictInterface-method | An Interface for survival Package's coxph Function
coxphRanking | Ranking of Differential Variability with coxph Statistic
coxphRanking-method | Ranking of Differential Variability with coxph Statistic
coxphTrainInterface | An Interface for survival Package's coxph Function
coxphTrainInterface-method | An Interface for survival Package's coxph Function
crossValidate | Cross-validation to evaluate classification performance.
crossValidate,MultiAssayExperiment-method, | Cross-validation to evaluate classification performance.
crossValidate-method | Cross-validation to evaluate classification performance.
CrossValParams | Parameters for Cross-validation Specification
CrossValParams-class | Parameters for Cross-validation Specification

## -- D --

DataFrameOrNULL | Union of NULL and DataFrame Class
DataFrameOrNULL-class | Union of NULL and DataFrame Class
differentMeansRanking | Ranking of Differentially Abundant Features
differentMeansRanking-method | Ranking of Differentially Abundant Features
distribution | Get Frequencies of Feature Selection and Sample-wise Classification Errors
distribution-method | Get Frequencies of Feature Selection and Sample-wise Classification Errors
dlda | Trained dlda Object
DLDA Interface | An Interface for sparsediscrim Package's dlda Function
dlda-class | Trained dlda Object
DLDApredictInterface | An Interface for sparsediscrim Package's dlda Function
DLDApredictInterface-method | An Interface for sparsediscrim Package's dlda Function
DLDAtrainInterface | An Interface for sparsediscrim Package's dlda Function
DLDAtrainInterface-method | An Interface for sparsediscrim Package's dlda Function
DMDranking | Ranking by Differential Distributions with Differences in Means or Medians and a Deviation Measure
DMDranking-method | Ranking by Differential Distributions with Differences in Means or Medians and a Deviation Measure

## -- E --

edgeRranking | Feature Ranking Based on Differential Expression for Count Data
edgeRranking-method | Feature Ranking Based on Differential Expression for Count Data
edgesToHubNetworks | Convert a Two-column Matrix or Data Frame into a Hub Node List
elasticNetFeatures | Extract Vectors of Ranked and Selected Features From an Elastic Net GLM Object
elasticNetFeatures-method | Extract Vectors of Ranked and Selected Features From an Elastic Net GLM Object
elasticNetGLMinterface | An Interface for glmnet Package's glmnet Function
elasticNetGLMpredictInterface | An Interface for glmnet Package's glmnet Function
elasticNetGLMpredictInterface-method | An Interface for glmnet Package's glmnet Function
elasticNetGLMtrainInterface | An Interface for glmnet Package's glmnet Function
elasticNetGLMtrainInterface-method | An Interface for glmnet Package's glmnet Function

## -- F --

features | Container for Storing Classification Results
features-method | Container for Storing Classification Results
FeatureSetCollection | Container for Storing A Collection of Sets
FeatureSetCollection-class | Container for Storing A Collection of Sets
FeatureSetCollection-method | Container for Storing A Collection of Sets
FeatureSetCollectionOrNULL | Union of a FeatureSetCollection and NULL
FeatureSetCollectionOrNULL-class | Union of a FeatureSetCollection and NULL
featureSetSummary | Transform a Table of Feature Abundances into a Table of Feature Set Abundances.
featureSetSummary-method | Transform a Table of Feature Abundances into a Table of Feature Set Abundances.
fisherDiscriminant | Classification Using Fisher's LDA
fisherDiscriminant-method | Classification Using Fisher's LDA
forestFeatures | Extract Vectors of Ranked and Selected Features From a Random Forest Object
forestFeatures-method | Extract Vectors of Ranked and Selected Features From a Random Forest Object
functionOrList | Union of Functions and List of Functions
functionOrList-class | Union of Functions and List of Functions
functionOrNULL | Union of A Function and NULL
functionOrNULL-class | Union of A Function and NULL

## -- G --

generateCrossValParams | A function to generate a CrossValParams object
generateModellingParams | A function to generate a ModellingParams object
getLocationsAndScales | Calculate Location and Scale
getLocationsAndScales-method | Calculate Location and Scale

## -- H --

HuRI | Human Reference Interactome

## -- I --

interactorDifferences | Convert Individual Features into Differences Between Binary Interactors Based on Known Sub-networks
interactorDifferences-method | Convert Individual Features into Differences Between Binary Interactors Based on Known Sub-networks
interactors | Human Reference Interactome

## -- K --

kNNinterface | An Interface for class Package's knn Function
kNNinterface-method | An Interface for class Package's knn Function
KolmogorovSmirnovRanking | Ranking of Differential Distributions with Kolmogorov-Smirnov Distance
KolmogorovSmirnovRanking-method | Ranking of Differential Distributions with Kolmogorov-Smirnov Distance
kTSPclassifier | Classification Using k Pairs of Features With Relative Differences Between Classes
kTSPclassifier-method | Classification Using k Pairs of Features With Relative Differences Between Classes
KullbackLeiblerRanking | Ranking of Differential Distributions with Kullback-Leibler Distance
KullbackLeiblerRanking-method | Ranking of Differential Distributions with Kullback-Leibler Distance

## -- L --

length-method | Container for Storing A Collection of Sets
leveneRanking | Selection of Differential Variability with Levene Statistic
leveneRanking-method | Selection of Differential Variability with Levene Statistic
likelihoodRatioRanking | Ranking of Differential Distributions with Likelihood Ratio Statistic
likelihoodRatioRanking-method | Ranking of Differential Distributions with Likelihood Ratio Statistic
limmaRanking | Ranking of Differentially Abundant Features
limmaRanking-method | Ranking of Differentially Abundant Features
listOrNULL | Union of a List and NULL
listOrNULL-class | Union of a List and NULL

## -- M --

measurements | Asthma RNA Abundance and Patient Classes
mixmodels | Classification based on Differential Distribution utilising Mixtures of Normals
mixModelsPredict | Classification based on Differential Distribution utilising Mixtures of Normals
mixModelsPredict-method | Classification based on Differential Distribution utilising Mixtures of Normals
mixModelsTrain | Classification based on Differential Distribution utilising Mixtures of Normals
mixModelsTrain-method | Classification based on Differential Distribution utilising Mixtures of Normals
ModellingParams | Parameters for Data Modelling Specification
ModellingParams-class | Parameters for Data Modelling Specification
ModellingParamsOrNULL | Union of A ModellingParams Object and NULL
ModellingParamsOrNULL-class | Union of A ModellingParams Object and NULL
models | Container for Storing Classification Results
models-method | Container for Storing Classification Results
multnet | Trained multnet Object
multnet-class | Trained multnet Object

## -- N --

naiveBayesKernel | Classification Using A Bayes Classifier with Kernel Density Estimates
naiveBayesKernel-method | Classification Using A Bayes Classifier with Kernel Density Estimates
NSCfeatures | Interface for 'pamr.train' Function from 'pamr' CRAN Package
NSCfeatures-method | Interface for 'pamr.train' Function from 'pamr' CRAN Package
NSCpredictInterface | Interface for 'pamr.train' Function from 'pamr' CRAN Package
NSCpredictInterface-method | Interface for 'pamr.train' Function from 'pamr' CRAN Package
NSCtrainInterface | Interface for 'pamr.train' Function from 'pamr' CRAN Package
NSCtrainInterface-method | Interface for 'pamr.train' Function from 'pamr' CRAN Package
numericOrNULL | Union of A Numeric Value and NULL
numericOrNULL-class | Union of A Numeric Value and NULL

## -- P --

pairsDifferencesRanking | Ranking of Pairs of Features that are Different Between Classes
pairsDifferencesRanking-method | Ranking of Pairs of Features that are Different Between Classes
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, Scatterplot, Parallel Plot or Bar Chart for Features By Class
plotFeatureClasses-method | Plot Density, Scatterplot, Parallel Plot or Bar Chart for Features By Class
predict-method | Cross-validation to evaluate classification performance.
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
PredictParamsOrNULL | Union of A PredictParams Object and NULL
PredictParamsOrNULL-class | Union of A PredictParams Object and NULL
previousSelection | Automated Selection of Previously Selected Features
previousSelection-method | Automated Selection of Previously Selected Features
previousTrained | Automated Usage of Previously Created Classifiers
previousTrained-method | Automated Usage of Previously Created Classifiers

## -- R --

randomForest | Trained randomForest Object
randomForest-class | Trained randomForest Object
randomForestInterfaces | An Interface for randomForest Package's randomForest Function
randomForestPredictInterface | An Interface for randomForest Package's randomForest Function
randomForestPredictInterface-method | An Interface for randomForest Package's randomForest Function
randomForestTrainInterface | An Interface for randomForest Package's randomForest Function
randomForestTrainInterface-method | An Interface for randomForest Package's randomForest Function
rankingPlot | Plot Pair-wise Overlap of Ranked Features
rankingPlot-method | Plot Pair-wise Overlap of Ranked Features
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

## -- S --

sampleNames | Container for Storing Classification Results
sampleNames-method | Container for Storing Classification Results
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, Variable Importance or Selection Size Distribution of Selected Features
selectionPlot-method | Plot Pair-wise Overlap, Variable Importance or Selection Size Distribution of Selected Features
SelectParams | Parameters for Feature Selection
SelectParams-class | Parameters for Feature Selection
SelectParams-method | Parameters for Feature Selection
SelectParamsOrNULL | Union of A SelectParams Object and NULL
SelectParamsOrNULL-class | Union of A SelectParams Object and NULL
show-method | Container for Storing Classification Results
show-method | Container for Storing A Collection of Sets
show-method | Parameters for Classifier Prediction
show-method | Parameters for Feature Selection
show-method | Parameters for Classifier Training
show-method | Parameters for Data Transformation
StageParams | StageParams Virtual Class
StageParams-class | StageParams Virtual Class
StageParamsOrMissing | Union of A StageParams Object and NULL
StageParamsOrMissing-class | Union of A StageParams Object and NULL
StageParamsOrMissingOrNULL | Union of A StageParams Object and NULL
StageParamsOrMissingOrNULL-class | Union of A StageParams Object and NULL
subtractFromLocation | Subtract Numeric Feature Measurements from a Location
subtractFromLocation-method | Subtract Numeric Feature Measurements from a Location
Surv | Survival Data Container
Surv-class | Survival Data Container
svm | Trained svm Object
svm-class | Trained svm Object
SVMpredictInterface | An Interface for e1071 Package's Support Vector Machine Classifier.
SVMpredictInterface-method | An Interface for e1071 Package's Support Vector Machine Classifier.
SVMtrainInterface | An Interface for e1071 Package's Support Vector Machine Classifier.
SVMtrainInterface-method | An Interface for e1071 Package's Support Vector Machine Classifier.

## -- T --

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
TransformParamsOrNULL | Union of A TransformParams Object and NULL
TransformParamsOrNULL-class | Union of A TransformParams Object and NULL
tunedParameters | Container for Storing Classification Results
tunedParameters-method | Container for Storing Classification Results

## -- misc --

[-method | Container for Storing A Collection of Sets
[[-method | Container for Storing A Collection of Sets