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

The package offer different classifiers based on comparisons of pair of features (TSP), using various decision rules (e.g., majority wins principle).

AuthorBahman Afsari <bahman@jhu.edu>, Luigi Marchionni <marchion@jhu.edu>, Wikum Dinalankara <wdinala1@jhmi.edu>
Date of publicationNone
MaintainerBahman Afsari <bahman@jhu.edu>, Luigi Marchionni <marchion@jhu.edu>, Wikum Dinalankara <wdinala1@jhmi.edu>
LicenseGPL-2
Version1.10.0

View on Bioconductor

Man pages

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

Files in this package

switchBox/DESCRIPTION
switchBox/NAMESPACE
switchBox/R
switchBox/R/exportedFuncs.R switchBox/R/forBackwardCompatibility.R switchBox/R/internalFuncs.R switchBox/R/miscFuncs.R switchBox/R/plotFuncs.R switchBox/R/utilFuncs.R
switchBox/build
switchBox/build/vignette.rds
switchBox/data
switchBox/data/testingData.rda
switchBox/data/trainingData.rda
switchBox/inst
switchBox/inst/CITATION
switchBox/inst/doc
switchBox/inst/doc/switchBox.R
switchBox/inst/doc/switchBox.Rnw
switchBox/inst/doc/switchBox.bib
switchBox/inst/doc/switchBox.pdf
switchBox/man
switchBox/man/KTSP.Classify.Rd switchBox/man/KTSP.Train.Rd switchBox/man/SWAP.Calculate.BasicTSPScores.Rd switchBox/man/SWAP.Calculate.SignedTSPScores.Rd switchBox/man/SWAP.CalculateScores.Rd switchBox/man/SWAP.CalculateSignedScore.Rd switchBox/man/SWAP.Filter.Wilcoxon.Rd switchBox/man/SWAP.GetKTSP.PredictionStats.Rd switchBox/man/SWAP.GetKTSP.Result.Rd switchBox/man/SWAP.GetKTSP.TrainTestResults.Rd switchBox/man/SWAP.KTSP.CV.Rd switchBox/man/SWAP.KTSP.Classify.Rd switchBox/man/SWAP.KTSP.LOO.Rd switchBox/man/SWAP.KTSP.Statistic.Rd switchBox/man/SWAP.KTSP.Train.Rd switchBox/man/SWAP.Kby.Measurement.Rd switchBox/man/SWAP.Kby.Ttest.Rd switchBox/man/SWAP.MakeTSPTable.Rd switchBox/man/SWAP.PlotKTSP.GenePairBoxplot.Rd switchBox/man/SWAP.PlotKTSP.GenePairClassesBoxplot.Rd switchBox/man/SWAP.PlotKTSP.GenePairScatter.Rd switchBox/man/SWAP.PlotKTSP.Genes.Rd switchBox/man/SWAP.PlotKTSP.TrainTestROC.Rd switchBox/man/SWAP.PlotKTSP.Votes.Rd switchBox/man/SWAP.Train.1TSP.Rd switchBox/man/SWAP.Train.KTSP.Rd switchBox/man/matTesting.Rd switchBox/man/matTraining.Rd switchBox/man/switchBox-package.Rd switchBox/man/testingGroup.Rd switchBox/man/trainingGroup.Rd
switchBox/src
switchBox/src/CalculateSignedScoreCore.cc
switchBox/src/CalculateSignedScoreCoreTieHandler.cc
switchBox/src/CalculateSignedScoreRestrictedPairsCore.cc
switchBox/src/CalculateSignedScoreRestrictedPairsCoreTieHandler.cc
switchBox/src/rinit.c
switchBox/src/vect2compC.cc
switchBox/vignettes
switchBox/vignettes/switchBox.Rnw
switchBox/vignettes/switchBox.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.