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

Documentation for package ‘ClassifyR’ version 3.0.3

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-- 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