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

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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.

Author
Dario Strbenac, John Ormerod, Graham Mann, Jean Yang
Date of publication
None
Maintainer
Dario Strbenac <dario.strbenac@sydney.edu.au>
License
GPL-3
Version
1.8.0

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