Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm

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Documentation for package ‘switchBox’ version 1.26.0

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switchBox-package A package to train and apply K-Top-Scoring-Pair (KTSP) classifiers.
KTSP.Classify Function to classify samples using a KTSP classifier.
KTSP.Train Funtion for training the K-TSP classifier.
matTesting Gene expression matrix for test set data
matTraining Gene expression matrix for training set data
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.Kby.Measurement K selection for a kTSP classifier.
SWAP.Kby.Ttest K selection for a kTSP classifier.
SWAP.KTSP.Classify Function to classify samples using a KTSP classifier.
SWAP.KTSP.CV Performs k-fold cross validation.
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.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.
switchBox A package to train and apply K-Top-Scoring-Pair (KTSP) classifiers.
testingGroup Testing set phenotypes
trainingGroup Training set phenotypes