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 2.12.0

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

-- 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 --

differentMeansSelection Selection of Differentially Abundant Features
differentMeansSelection-method Selection of Differentially Abundant Features
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 --

EasyHardClassifier Container for a Pair of Trained Classifiers
easyHardClassifier Two-stage Classification Using Easy-to-collect Data Set and Hard-to-collect data set.
EasyHardClassifier-class Container for a Pair of Trained Classifiers
EasyHardClassifier-method Container for a Pair of Trained Classifiers
easyHardClassifierPredict Two-stage Classification Using Easy-to-collect Data Set and Hard-to-collect data set.
easyHardClassifierPredict-method Two-stage Classification Using Easy-to-collect Data Set and Hard-to-collect data set.
easyHardClassifierTrain Two-stage Classification Using Easy-to-collect Data Set and Hard-to-collect data set.
easyHardClassifierTrain-method Two-stage Classification Using Easy-to-collect Data Set and Hard-to-collect data set.
easyHardFeatures Extract Chosen Features from an EasyHardClassifier Object
easyHardFeatures-method Extract Chosen Features from an EasyHardClassifier Object
edgeRselection Feature Selection Based on Differential Expression for Count Data
edgeRselection-method Feature Selection 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 --

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
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 --

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

-- I --

integerOrNumeric Union of a Integer and a Numeric
integerOrNumeric-class Union of a Integer and a Numeric
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

-- K --

kNNinterface An Interface for class Package's knn Function
kNNinterface-method An Interface for class Package's knn Function
KolmogorovSmirnovSelection Selection of Differential Distributions with Kolmogorov-Smirnov Distance
KolmogorovSmirnovSelection-method Selection 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
KullbackLeiblerSelection Selection of Differential Distributions with Kullback-Leibler Distance
KullbackLeiblerSelection-method Selection of Differential Distributions with Kullback-Leibler Distance

-- L --

length-method Container for Storing A Collection of Sets
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
listOrCharacterOrNULL Union of a List and a Character Vector and NULL
listOrCharacterOrNULL-class Union of a List and a Character Vector and NULL
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
MixModelsListsSet Container for a List of Lists Containing Mixture Models
MixModelsListsSet-class Container for a List of Lists Containing Mixture Models
MixModelsListsSet-method Container for a List of Lists Containing Mixture Models
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
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
networkCorrelationsSelection Selection of Differentially Correlated Hub Sub-networks
networkCorrelationsSelection-method Selection of Differentially Correlated Hub Sub-networks
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 --

pairsDifferencesSelection Selection of Pairs of Features that are Different Between Classes
pairsDifferencesSelection-method Selection 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
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
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
randomForestInterface 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
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
runTestEasyHard Perform a Single Classification
runTestEasyHard-method Perform a Single Classification
runTests Reproducibly Run Various Kinds of Cross-Validation
runTests-method Reproducibly Run Various Kinds of Cross-Validation
runTestsEasyHard Reproducibly Run Various Kinds of Cross-Validation
runTestsEasyHard-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 a Pair of Trained Classifiers
show-method Container for Storing A Collection of Sets
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

-- misc --

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