KTSP.Classify           Function to classify samples using a KTSP
                        classifier.
KTSP.Train              Funtion for training the K-TSP classifier.
SWAP.Calculate.BasicTSPScores
                        Function to calculate basic TSP scores.
SWAP.Calculate.SignedTSPScores
                        Function to calculate signed TSP scores.
SWAP.CalculateScores    Function to calculate the pair-wise scores with
                        any given score function.
SWAP.CalculateSignedScore
                        Function to calculate the pair-wise scores.
SWAP.Filter.Wilcoxon    Statistical feature filtering based on Wilcoxon
                        test on the ranks of expressions.
SWAP.GetKTSP.PredictionStats
                        Function for computing various performance
                        measures related to prediction.
SWAP.GetKTSP.Result     Function for prediction followed by computing
                        various performance measures related to
                        prediction.
SWAP.GetKTSP.TrainTestResults
                        Trains a kTSP on given training data and
                        provides performance on testing data.
SWAP.KTSP.CV            Performs k-fold cross validation.
SWAP.KTSP.Classify      Function to classify samples using a KTSP
                        classifier.
SWAP.KTSP.LOO           Performs leave one out cross validation.
SWAP.KTSP.Statistics    Function computing TSP votes (comparisons) and
                        combine their votes. The default is the kTSP
                        statistics, sum of the votes.
SWAP.KTSP.Train         Deprecated function for training the K-TSP
                        classifier.
SWAP.Kby.Measurement    K selection for a kTSP classifier.
SWAP.Kby.Ttest          K selection for a kTSP classifier.
SWAP.MakeTSPTable       Make a table of TSPs in order of TSP score.
SWAP.PlotKTSP.GenePairBoxplot
                        Plots a feature pair as boxplots.
SWAP.PlotKTSP.GenePairClassesBoxplot
                        Plots a feature pair as seperated by class as
                        boxplots.
SWAP.PlotKTSP.GenePairScatter
                        Make a scatter plot of two features.
SWAP.PlotKTSP.Genes     Plot features seperated by phenotype
SWAP.PlotKTSP.TrainTestROC
                        Plots an ROC curve for training and testing
                        results.
SWAP.PlotKTSP.Votes     Plots a heatmap of k-TSP votes.
SWAP.Train.1TSP         Function for training the 1-TSP classifier.
SWAP.Train.KTSP         Function for training the K-TSP classifier.
matTesting              Gene expression matrix for test set data
matTraining             Gene expression matrix for training set data
switchBox-package       A package to train and apply K-Top-Scoring-Pair
                        (KTSP) classifiers.
testingGroup            Testing set phenotypes
trainingGroup           Training set phenotypes
