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


[Up] [Top]

Documentation for package ‘ClassifyR’ version 1.12.2

Help Pages

actualClasses Container for Storing Classification Results
actualClasses-method Container for Storing Classification Results
bartlettSelection Selection of Differential Variability with Bartlett Statistic
bartlettSelection-method Selection of Differential Variability with Bartlett Statistic
calcPerformance Add Performance Calculations to a ClassifyResult object
calcPerformance-method Add Performance Calculations to a ClassifyResult object
classifyInterface 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
distribution Get Frequencies of Feature Selection and Sample Errors
distribution-method Get Frequencies of Feature Selection and Sample Errors
DMDselection Selection of Differential Distributions with Differences in Means or Medians and a Deviation Measure
DMDselection-method Selection of Differential Distributions with Differences in Means or Medians and a Deviation Measure
edgeRselection Feature Selection Based on Differential Expression for RNA-seq
edgeRselection-method Feature Selection Based on Differential Expression for RNA-seq
features Container for Storing Classification Results
features-method Container for Storing Classification Results
fisherDiscriminant Classification Using Fisher's LDA
fisherDiscriminant-method Classification Using Fisher's LDA
functionOrList Union of Functions and List of Functions
functionOrList-class Union of Functions and List of Functions
getLocationsAndScales Calculate Location and Scale
getLocationsAndScales-method Calculate Location and Scale
KolmogorovSmirnovSelection Selection of Differential Distributions with Kolmogorov-Smirnov Distance
KolmogorovSmirnovSelection-method Selection of Differential Distributions with Kolmogorov-Smirnov Distance
KullbackLeiblerSelection Selection of Differential Distributions with Kullback Leibler Distance
KullbackLeiblerSelection-method Selection of Differential Distributions with Kullback Leibler Distance
leveneSelection Selection of Differential Variability with Levene Statistic
leveneSelection-method Selection of Differential Variability with Levene Statistic
likelihoodRatioSelection Selection of Differential Distributions with Likelihood Ratio Statistic
likelihoodRatioSelection-method Selection of Differential Distributions with Likelihood Ratio Statistic
limmaSelection Selection of Differentially Expressed Features
limmaSelection-method Selection of Differentially Expressed Features
medianDifferenceSelection Selection of Differential Expression by Comparing Differences in Medians of Groups
medianDifferenceSelection-method Selection of Differential Expression by Comparing Differences in Medians of Groups
mixmodels Selection of Differential Distributions with Mixtures of Normals
mixModelsTest Selection of Differential Distributions with Mixtures of Normals
mixModelsTest-method Selection of Differential Distributions with Mixtures of Normals
mixModelsTrain Selection of Differential Distributions with Mixtures of Normals
mixModelsTrain-method Selection of Differential Distributions with Mixtures of Normals
naiveBayesKernel Classification Using A Bayes Classifier with Kernel Density Estimates
naiveBayesKernel-method Classification Using A Bayes Classifier with Kernel Density Estimates
nearestShrunkenCentroidPredictInterface Interface for 'pamr.predict' Function from 'pamr' CRAN Package
nearestShrunkenCentroidPredictInterface-method Interface for 'pamr.predict' Function from 'pamr' CRAN Package
nearestShrunkenCentroidSelectionInterface Interface for 'pamr.listgenes' Function from 'pamr' CRAN Package
nearestShrunkenCentroidSelectionInterface-method Interface for 'pamr.listgenes' Function from 'pamr' CRAN Package
nearestShrunkenCentroidTrainInterface Interface for 'pamr.train' Function from 'pamr' CRAN Package
nearestShrunkenCentroidTrainInterface-method Interface for 'pamr.train' Function from 'pamr' CRAN Package
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 and Scatterplot for Genes By Class
plotFeatureClasses-method Plot Density and Scatterplot for Genes By Class
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
previousSelection Automated Selection of Previously Selected Features
previousSelection-method Automated Selection of Previously Selected Features
rankingPlot Plot Pair-wise Overlap of Ranked Features
rankingPlot-method Plot Pair-wise Overlap of Ranked Features
ResubstituteParams Parameters for Resubstitution Error Calculation
ResubstituteParams-class Parameters for Resubstitution Error Calculation
ResubstituteParams-method Parameters for Resubstitution Error Calculation
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
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 or Selection Size Distribution of Selected Features
selectionPlot-method Plot Pair-wise Overlap or Selection Size Distribution of Selected Features
SelectParams Parameters for Feature Selection
SelectParams-class Parameters for Feature Selection
SelectParams-method Parameters for Feature Selection
SelectResult Container for Storing Feature Selection Results
SelectResult-class Container for Storing Feature Selection Results
SelectResult-method Container for Storing Feature Selection Results
show-method Container for Storing Classification Results
show-method Container for Storing Feature Selection Results
subtractFromLocation Subtract All Feature Measurements from Location
subtractFromLocation-method Subtract All Feature Measurements from Location
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
tunedParameters Container for Storing Classification Results
tunedParameters-method Container for Storing Classification Results