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

The software formalises a framework for classification in R. There are four stages; Data transformation, feature selection, classifier training, and prediction. The requirements of variable types and names are fixed, but specialised variables for functions can also be provided. The classification framework is wrapped in a driver loop, that reproducibly carries out a number of cross-validation schemes. Functions for differential expression, differential variability, and differential distribution are included. Additional functions may be developed by the user, by creating an interface to the framework.

AuthorDario Strbenac, John Ormerod, Graham Mann, Jean Yang
Date of publicationNone
MaintainerDario Strbenac <dario.strbenac@sydney.edu.au>
LicenseGPL-3
Version1.8.2

View on Bioconductor

Man pages

bartlettSelection: Selection of Differential Variability with Bartlett Statistic

calcPerformance: Add Performance Calculations to a ClassifyResult object

classifyInterface: Interface for PoiClaClu Package's Classify Function

ClassifyResult-class: Container for Storing Classification Results

distribution: Get Frequencies of Feature Selection and Sample Errors

DMDselection: Selection of Differential Distributions with Differences in...

edgeRselection: Feature Selection Based on Differential Expression for...

errorMap: Plot a Grid of Sample Error Rates

fisherDiscriminant: Classification Using Fisher's LDA

functionOrList-class: Union of Functions and List of Functions

getLocationsAndScales: Calculate Location and Scale

KolmogorovSmirnovSelection: Selection of Differential Distributions with...

KullbackLeiblerSelection: Selection of Differential Distributions with Kullback Leibler...

leveneSelection: Selection of Differential Variability with Levene Statistic

likelihoodRatioSelection: Selection of Differential Distributions with Likelihood Ratio...

limmaSelection: Selection of Differentially Expressed Features

medianDifferenceSelection: Selection of Differential Expression by Comparing Differences...

mixmodels: Selection of Differential Distributions with Mixtures of...

naiveBayesKernel: Classification Using A Bayes Classifier with Kernel Density...

nearestShrunkenCentroidPredictInterface: Interface for 'pamr.predict' Function from 'pamr' CRAN...

nearestShrunkenCentroidSelectionInterface: Interface for 'pamr.listgenes' Function from 'pamr' CRAN...

nearestShrunkenCentroidTrainInterface: Interface for 'pamr.train' Function from 'pamr' CRAN Package

pamrtrained-class: Trained pamr Object

performancePlot: Plot Performance Measures for Various Classifications

plotFeatureClasses: Plot Density and Scatterplot for Genes By Class

PredictParams-class: Parameters for Classifier Prediction

previousSelection: Automated Selection of Previously Selected Features

rankingPlot: Plot Pair-wise Overlap of Ranked Features

ResubstituteParams-class: Parameters for Resubstitution Error Calculation

ROCplot: Plot Receiver Operating Curve Graphs for Classification...

runTest: Perform a Single Classification

runTests: Reproducibly Run Various Kinds of Cross-Validation

selectionPlot: Plot Pair-wise Overlap or Selection Size Distribution of...

SelectParams-class: Parameters for Feature Selection

SelectResult-class: Container for Storing Feature Selection Results

subtractFromLocation: Subtract All Feature Measurements from Location

TrainParams-class: Parameters for Classifier Training

TransformParams-class: Parameters for Data Transformation

Functions

actualClasses Man page
actualClasses,ClassifyResult-method Man page
bartlettSelection Man page
bartlettSelection,ExpressionSet-method Man page
bartlettSelection,matrix-method Man page
calcPerformance Man page
calcPerformance,ClassifyResult-method Man page
classifyInterface Man page
ClassifyResult Man page
ClassifyResult,character,character,character,character,character Man page
ClassifyResult-class Man page
distribution Man page
distribution,ClassifyResult-method Man page
DMDselection Man page
DMDselection,ExpressionSet-method Man page
DMDselection,matrix-method Man page
edgeRselection Man page
edgeRselection,ExpressionSet-method Man page
edgeRselection,matrix-method Man page
errorMap Man page
errorMap,list-method Man page
features Man page
features,ClassifyResult-method Man page
fisherDiscriminant Man page
fisherDiscriminant,ExpressionSet-method Man page
fisherDiscriminant,matrix-method Man page
functionOrList Man page
functionOrList-class Man page
getLocationsAndScales Man page
getLocationsAndScales,ExpressionSet-method Man page
getLocationsAndScales,matrix-method Man page
KolmogorovSmirnovSelection Man page
KolmogorovSmirnovSelection,ExpressionSet-method Man page
KolmogorovSmirnovSelection,matrix-method Man page
KullbackLeiblerSelection Man page
KullbackLeiblerSelection,ExpressionSet-method Man page
KullbackLeiblerSelection,matrix-method Man page
leveneSelection Man page
leveneSelection,ExpressionSet-method Man page
leveneSelection,matrix-method Man page
likelihoodRatioSelection Man page
likelihoodRatioSelection,ExpressionSet-method Man page
likelihoodRatioSelection,matrix-method Man page
limmaSelection Man page
limmaSelection,ExpressionSet-method Man page
limmaSelection,matrix-method Man page
medianDifferenceSelection Man page
medianDifferenceSelection,ExpressionSet-method Man page
medianDifferenceSelection,matrix-method Man page
mixmodels Man page
mixModelsTest Man page
mixModelsTest,list,ExpressionSet-method Man page
mixModelsTest,list,matrix-method Man page
mixModelsTrain Man page
mixModelsTrain,ExpressionSet-method Man page
mixModelsTrain,matrix-method Man page
naiveBayesKernel Man page
naiveBayesKernel,ExpressionSet-method Man page
naiveBayesKernel,matrix-method Man page
nearestShrunkenCentroidPredictInterface Man page
nearestShrunkenCentroidPredictInterface,pamrtrained,ExpressionSe Man page
nearestShrunkenCentroidPredictInterface,pamrtrained,matrix-metho Man page
nearestShrunkenCentroidSelectionInterface Man page
nearestShrunkenCentroidSelectionInterface,ExpressionSet-method Man page
nearestShrunkenCentroidSelectionInterface,matrix-method Man page
nearestShrunkenCentroidTrainInterface Man page
nearestShrunkenCentroidTrainInterface,ExpressionSet-method Man page
nearestShrunkenCentroidTrainInterface,matrix-method Man page
pamrtrained Man page
pamrtrained-class Man page
performance Man page
performance,ClassifyResult-method Man page
performancePlot Man page
performancePlot,list-method Man page
plotFeatureClasses Man page
plotFeatureClasses,ExpressionSet-method Man page
plotFeatureClasses,matrix-method Man page
predictions Man page
predictions,ClassifyResult-method Man page
PredictParams Man page
PredictParams,ANY-method Man page
PredictParams-class Man page
PredictParams,function-method Man page
previousSelection Man page
previousSelection,ExpressionSet-method Man page
previousSelection,matrix-method Man page
rankingPlot Man page
rankingPlot,list-method Man page
ResubstituteParams Man page
ResubstituteParams,ANY,ANY,ANY-method Man page
ResubstituteParams-class Man page
ResubstituteParams,numeric,character,character-method Man page
ROCplot Man page
ROCplot,list-method Man page
runTest Man page
runTest,ExpressionSet-method Man page
runTest,matrix-method Man page
runTests Man page
runTests,ExpressionSet-method Man page
runTests,matrix-method Man page
selectionPlot Man page
selectionPlot,list-method Man page
SelectParams Man page
SelectParams,ANY-method Man page
SelectParams-class Man page
SelectParams,functionOrList-method Man page
SelectResult Man page
SelectResult,character,character,list,list-method Man page
SelectResult-class Man page
show,ClassifyResult-method Man page
show,SelectResult-method Man page
subtractFromLocation Man page
subtractFromLocation,ExpressionSet-method Man page
subtractFromLocation,matrix-method Man page
totalPredictions Man page
totalPredictions,ClassifyResult-method Man page
TrainParams Man page
TrainParams,ANY-method Man page
TrainParams-class Man page
TrainParams,function-method Man page
TransformParams Man page
TransformParams,ANY-method Man page
TransformParams-class Man page
TransformParams,function-method Man page
tunedParameters Man page
tunedParameters,ClassifyResult-method Man page

Files

ClassifyR/DESCRIPTION
ClassifyR/NAMESPACE
ClassifyR/R
ClassifyR/R/DMDselection.R ClassifyR/R/KolmogorovSmirnovSelection.R ClassifyR/R/KullbackLeiblerSelection.R ClassifyR/R/ROCplot.R ClassifyR/R/bartlettSelection.R ClassifyR/R/calcPerformance.R ClassifyR/R/classes.R ClassifyR/R/classifyInterface.R ClassifyR/R/distribution.R ClassifyR/R/edgeRselection.R ClassifyR/R/errorMap.R ClassifyR/R/fisherDiscriminant.R ClassifyR/R/getLocationsAndScales.R ClassifyR/R/leveneSelection.R ClassifyR/R/likelihoodRatioSelection.R ClassifyR/R/limmaSelection.R ClassifyR/R/medianDifferenceSelection.R ClassifyR/R/mixmodels.R ClassifyR/R/naiveBayesKernel.R ClassifyR/R/nearestShrunkenCentroidPredictInterface.R ClassifyR/R/nearestShrunkenCentroidSelectionInterface.R ClassifyR/R/nearestShrunkenCentroidTrainInterface.R ClassifyR/R/performancePlot.R ClassifyR/R/plotFeatureClasses.R ClassifyR/R/previousSelection.R ClassifyR/R/rankingPlot.R ClassifyR/R/runTest.R ClassifyR/R/runTests.R ClassifyR/R/selectionPlot.R ClassifyR/R/subtractFromLocation.R ClassifyR/R/utilities.R
ClassifyR/build
ClassifyR/build/vignette.rds
ClassifyR/inst
ClassifyR/inst/CITATION
ClassifyR/inst/NEWS.Rd
ClassifyR/inst/doc
ClassifyR/inst/doc/ClassifyR.R
ClassifyR/inst/doc/ClassifyR.Rmd
ClassifyR/inst/doc/ClassifyR.html
ClassifyR/man
ClassifyR/man/ClassifyResult-class.Rd ClassifyR/man/DMDselection.Rd ClassifyR/man/KolmogorovSmirnovSelection.Rd ClassifyR/man/KullbackLeiblerSelection.Rd ClassifyR/man/PredictParams-class.Rd ClassifyR/man/ROCplot.Rd ClassifyR/man/ResubstituteParams-class.Rd ClassifyR/man/SelectParams-class.Rd ClassifyR/man/SelectResult-class.Rd ClassifyR/man/TrainParams-class.Rd ClassifyR/man/TransformParams-class.Rd ClassifyR/man/bartlettSelection.Rd ClassifyR/man/calcPerformance.Rd ClassifyR/man/classifyInterface.Rd ClassifyR/man/distribution.Rd ClassifyR/man/edgeRselection.Rd ClassifyR/man/errorMap.Rd ClassifyR/man/fisherDiscriminant.Rd ClassifyR/man/functionOrList-class.Rd ClassifyR/man/getLocationsAndScales.Rd ClassifyR/man/leveneSelection.Rd ClassifyR/man/likelihoodRatioSelection.Rd ClassifyR/man/limmaSelection.Rd ClassifyR/man/medianDifferenceSelection.Rd ClassifyR/man/mixmodels.Rd ClassifyR/man/naiveBayesKernel.Rd ClassifyR/man/nearestShrunkenCentroidPredictInterface.Rd ClassifyR/man/nearestShrunkenCentroidSelectionInterface.Rd ClassifyR/man/nearestShrunkenCentroidTrainInterface.Rd ClassifyR/man/pamrtrained-class.Rd ClassifyR/man/performancePlot.Rd ClassifyR/man/plotFeatureClasses.Rd ClassifyR/man/previousSelection.Rd ClassifyR/man/rankingPlot.Rd ClassifyR/man/runTest.Rd ClassifyR/man/runTests.Rd ClassifyR/man/selectionPlot.Rd ClassifyR/man/subtractFromLocation.Rd
ClassifyR/vignettes
ClassifyR/vignettes/ClassifyR.Rmd

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