The package offer different classifiers based on comparisons of pair of features (TSP), using various decision rules (e.g., majority wins principle).
|Author||Bahman Afsari <firstname.lastname@example.org>, Luigi Marchionni <email@example.com>, Wikum Dinalankara <firstname.lastname@example.org>|
|Date of publication||None|
|Maintainer||Bahman Afsari <email@example.com>, Luigi Marchionni <firstname.lastname@example.org>, Wikum Dinalankara <email@example.com>|
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.CalculateScores: Function to calculate the pair-wise scores with any given...
SWAP.CalculateSignedScore: Function to calculate the pair-wise scores.
SWAP.Calculate.SignedTSPScores: Function to calculate signed TSP scores.
SWAP.Filter.Wilcoxon: Statistical feature filtering based on Wilcoxon test on the...
SWAP.GetKTSP.PredictionStats: Function for computing various performance measures related...
SWAP.GetKTSP.Result: Function for prediction followed by computing various...
SWAP.GetKTSP.TrainTestResults: Trains a kTSP on given training data and provides performance...
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.Statistic: Function computing TSP votes (comparisons) and combine their...
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-package: A package to train and apply K-Top-Scoring-Pair (KTSP)...
testingGroup: Testing set phenotypes
trainingGroup: Training set phenotypes