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 1.43.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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