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

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Documentation for package ‘ClassifyR’ version 2.0.10

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

-- A --

actualClasses Container for Storing Classification Results
actualClasses-method Container for Storing Classification Results

-- B --

bartlettSelection Selection of Differential Variability with Bartlett Statistic
bartlettSelection-method Selection 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
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

-- D --

distribution Get Frequencies of Feature Selection and Sample Errors
distribution-method Get Frequencies of Feature Selection and Sample Errors
dlda Trained dlda Object
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
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

-- E --

edgeRselection Feature Selection Based on Differential Expression for Count Data
edgeRselection-method Feature Selection Based on Differential Expression for Count Data
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 --

featureNames Container for Storing Classification Results
featureNames-method Container for Storing Classification Results
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
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 --

getLocationsAndScales Calculate Location and Scale
getLocationsAndScales-method Calculate Location and Scale

-- K --

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

-- L --

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 Abundant Features
limmaSelection-method Selection of Differentially Abundant Features
logisticRegressionInterface An Interface for mnlogit Package's mnlogit Function
logisticRegressionPredictInterface An Interface for mnlogit Package's mnlogit Function
logisticRegressionPredictInterface-method An Interface for mnlogit Package's mnlogit Function
logisticRegressionTrainInterface An Interface for mnlogit Package's mnlogit Function
logisticRegressionTrainInterface-method An Interface for mnlogit Package's mnlogit Function

-- 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
mnlogit Trained mnlogit Object
mnlogit-class Trained mnlogit Object
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
NSCpredictInterface Interface for 'pamr.predict' Function from 'pamr' CRAN Package
NSCpredictInterface-method Interface for 'pamr.predict' Function from 'pamr' CRAN Package
NSCselectionInterface Interface for 'pamr.listgenes' Function from 'pamr' CRAN Package
NSCselectionInterface-method Interface for 'pamr.listgenes' 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

-- P --

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 or Bar Chart for Features By Class
plotFeatureClasses-method Plot Density, Scatterplot or Bar Chart for Features 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

-- R --

randomForest Trained randomForest Object
randomForest-class Trained randomForest Object
randomForestInterface An Interface for randomForest Package's randomForest Function
randomForestInterface-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
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

-- 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 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 Numeric Feature Measurements from a Location
subtractFromLocation-method Subtract Numeric Feature Measurements from a Location
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
tunedParameters Container for Storing Classification Results
tunedParameters-method Container for Storing Classification Results