ClassifyResult          Container for Storing Classification Results
CrossValParams          Parameters for Cross-validation Specification
DLDA Interface          An Interface for sparsediscrim Package's dlda
                        Function
DMDranking              Ranking by Differential Distributions with
                        Differences in Means or Medians and a Deviation
                        Measure
DataFrameOrNULL-class   Union of NULL and DataFrame Class
FeatureSetCollection    Container for Storing A Collection of Sets
FeatureSetCollectionOrNULL-class
                        Union of a FeatureSetCollection and NULL
HuRI                    Human Reference Interactome
KolmogorovSmirnovRanking
                        Ranking of Differential Distributions with
                        Kolmogorov-Smirnov Distance
KullbackLeiblerRanking
                        Ranking of Differential Distributions with
                        Kullback-Leibler Distance
ModellingParams         Parameters for Data Modelling Specification
ModellingParamsOrNULL-class
                        Union of A ModellingParams Object and NULL
NSCtrainInterface       Interface for 'pamr.train' Function from 'pamr'
                        CRAN Package
PredictParams           Parameters for Classifier Prediction
PredictParamsOrNULL     Union of A PredictParams Object and NULL
ROCplot                 Plot Receiver Operating Curve Graphs for
                        Classification Results
SVMtrainInterface       An Interface for e1071 Package's Support Vector
                        Machine Classifier.
SelectParams            Parameters for Feature Selection
SelectParamsOrNULL-class
                        Union of A SelectParams Object and NULL
StageParams-class       StageParams Virtual Class
StageParamsOrMissing-class
                        Union of A StageParams Object and NULL
Surv-class              Survival Data Container
TrainParams             Parameters for Classifier Training
TransformParams         Parameters for Data Transformation
TransformParamsOrNULL-class
                        Union of A TransformParams Object and NULL
asthma                  Asthma RNA Abundance and Patient Classes
bartlettRanking         Ranking of Differential Variability with
                        Bartlett Statistic
calcExternalPerformance
                        Add Performance Calculations to a
                        ClassifyResult Object or Calculate for a Pair
                        of Factor Vectors
characterOrDataFrame-class
                        Union of a Character and a DataFrame
classifyInterface       An Interface for PoiClaClu Package's Classify
                        Function
coxnetTrainInterface    An Interface for glmnet Package's coxnet
                        Function
coxph-class             Trained coxph Object
coxphRanking            Ranking of Differential Variability with coxph
                        Statistic
coxphTrainInterface     An Interface for survival Package's coxph
                        Function
crossValidate           Cross-validation to evaluate classification
                        performance.
differentMeansRanking   Ranking of Differentially Abundant Features
distribution            Get Frequencies of Feature Selection and
                        Sample-wise Classification Errors
dlda-class              Trained dlda Object
edgeRranking            Feature Ranking Based on Differential
                        Expression for Count Data
edgesToHubNetworks      Convert a Two-column Matrix or Data Frame into
                        a Hub Node List
elasticNetFeatures      Extract Vectors of Ranked and Selected Features
                        From an Elastic Net GLM Object
elasticNetGLMtrainInterface
                        An Interface for glmnet Package's glmnet
                        Function
featureSetSummary       Transform a Table of Feature Abundances into a
                        Table of Feature Set Abundances.
fisherDiscriminant      Classification Using Fisher's LDA
forestFeatures          Extract Vectors of Ranked and Selected Features
                        From a Random Forest Object
functionOrList-class    Union of Functions and List of Functions
functionOrNULL-class    Union of A Function and NULL
generateCrossValParams
                        A function to generate a CrossValParams object
generateModellingParams
                        A function to generate a ModellingParams object
getLocationsAndScales   Calculate Location and Scale
interactorDifferences   Convert Individual Features into Differences
                        Between Binary Interactors Based on Known
                        Sub-networks
kNNinterface            An Interface for class Package's knn Function
kTSPclassifier          Classification Using k Pairs of Features With
                        Relative Differences Between Classes
leveneRanking           Selection of Differential Variability with
                        Levene Statistic
likelihoodRatioRanking
                        Ranking of Differential Distributions with
                        Likelihood Ratio Statistic
limmaRanking            Ranking of Differentially Abundant Features
listOrNULL-class        Union of a List and NULL
mixModelsTrain          Classification based on Differential
                        Distribution utilising Mixtures of Normals
multnet-class           Trained multnet Object
naiveBayesKernel        Classification Using A Bayes Classifier with
                        Kernel Density Estimates
numericOrNULL-class     Union of A Numeric Value and NULL
pairsDifferencesRanking
                        Ranking of Pairs of Features that are Different
                        Between Classes
pamrtrained-class       Trained pamr Object
performancePlot         Plot Performance Measures for Various
                        Classifications
plotFeatureClasses      Plot Density, Scatterplot, Parallel Plot or Bar
                        Chart for Features By Class
previousSelection       Automated Selection of Previously Selected
                        Features
previousTrained         Automated Usage of Previously Created
                        Classifiers
randomForest-class      Trained randomForest Object
randomForestInterfaces
                        An Interface for randomForest Package's
                        randomForest Function
rankingPlot             Plot Pair-wise Overlap of Ranked Features
runTest                 Perform a Single Classification
runTests                Reproducibly Run Various Kinds of
                        Cross-Validation
samplesMetricMap        Plot a Grid of Sample Error Rates or Accuracies
selectionPlot           Plot Pair-wise Overlap, Variable Importance or
                        Selection Size Distribution of Selected
                        Features
subtractFromLocation    Subtract Numeric Feature Measurements from a
                        Location
svm-class               Trained svm Object
