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

Functions

KTSP.Classify Man page
KTSP.Train Man page
matTesting Man page
matTraining Man page
SWAP.Calculate.BasicTSPScores Man page
SWAP.CalculateScores Man page
SWAP.CalculateSignedScore Man page
SWAP.Calculate.SignedTSPScores Man page
SWAP.Filter.Wilcoxon Man page
SWAP.GetKTSP.PredictionStats Man page
SWAP.GetKTSP.Result Man page
SWAP.GetKTSP.TrainTestResults Man page
SWAP.Kby.Measurement Man page
SWAP.Kby.Ttest Man page
SWAP.KTSP.Classify Man page
SWAP.KTSP.CV Man page
SWAP.KTSP.LOO Man page
SWAP.KTSP.Statistics Man page
SWAP.KTSP.Train Man page
SWAP.MakeTSPTable Man page
SWAP.PlotKTSP.GenePairBoxplot Man page
SWAP.PlotKTSP.GenePairClassesBoxplot Man page
SWAP.PlotKTSP.GenePairScatter Man page
SWAP.PlotKTSP.Genes Man page
SWAP.PlotKTSP.TrainTestROC Man page
SWAP.PlotKTSP.Votes Man page
SWAP.Train.1TSP Man page
SWAP.Train.KTSP Man page
switchBox Man page
switchBox-package Man page
testingGroup Man page
trainingGroup Man page

Files

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

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