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ClassifyR (version 1.6.2)

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

Description

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.

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Version

Version

1.6.2

License

GPL-3

Maintainer

Dario Strbenac

Last Published

February 15th, 2017

Functions in ClassifyR (1.6.2)

KolmogorovSmirnovSelection

Selection of Differential Distributions with Kolmogorov-Smirnov Distance
DMDselection

Selection of Differential Distributions with Differences in Means or Medians and a Deviation Measure
distribution

Get Frequencies of Feature Selection and Sample Errors
ROCplot

Plot Receiver Operating Curve Graphs for Classification Results
limmaSelection

Selection of Differentially Expressed Features
KullbackLeiblerSelection

Selection of Differential Distributions with Kullback Leibler Distance
naiveBayesKernel

Classification Using A Bayes Classifier with Kernel Density Estimates
errorMap

Plot a Grid of Sample Error Rates
selectionPlot

Plot Pair-wise Overlap or Selection Size Distribution of Selected Features
SelectParams

Parameters for Feature Selection
nearestShrunkenCentroidSelectionInterface

Interface for pamr.listgenes Function from pamr CRAN Package
TrainParams

Parameters for Classifier Training
likelihoodRatioSelection

Selection of Differential Distributions with Likelihood Ratio Statistic
edgeRselection

Feature Selection Based on Differential Expression for RNA-seq
performancePlot

Plot Performance Measures for Various Classifications
leveneSelection

Selection of Differential Variability with Levene Statistic
runTests

Reproducibly Do Resampling or Leave Out and Cross Validation
previousSelection

Automated Selection of Previously Selected Features
bartlettSelection

Selection of Differential Variability with Bartlett Statistic
TransformParams

Parameters for Data Transformation
runTest

Perform a Single Classification
classifyInterface

Interface for PoiClaClu Package's Classify Function
fisherDiscriminant

Classification Using Fisher's LDA
PredictParams

Parameters for Classifier Prediction
plotFeatureClasses

Plot Density and Scatterplot for Genes By Class
pamrtrained

Trained pamr Object
nearestShrunkenCentroidTrainInterface

Interface for pamr.train Function from pamr CRAN Package
nearestShrunkenCentroidPredictInterface

Interface for pamr.predict Function from pamr CRAN Package
functionOrList

Union of Functions and List of Functions
ResubstituteParams

Parameters for Resubstitution Error Calculation
rankingPlot

Plot Pair-wise Overlap of Ranked Features
ClassifyResult

Container for Storing Classification Results
SelectResult

Container for Storing Feature Selection Results
calcPerformance

Add Performance Calculations to a ClassifyResult object
mixmodels

Selection of Differential Distributions with Mixtures of Normals
subtractFromLocation

Subtract All Feature Measurements from Location
getLocationsAndScales

Calculate Location and Scale