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
Version1.8.1

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

Files in this package

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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