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).

Author
Bahman Afsari <bahman@jhu.edu>, Luigi Marchionni <marchion@jhu.edu>, Wikum Dinalankara <wdinala1@jhmi.edu>
Date of publication
None
Maintainer
Bahman Afsari <bahman@jhu.edu>, Luigi Marchionni <marchion@jhu.edu>, Wikum Dinalankara <wdinala1@jhmi.edu>
License
GPL-2
Version
1.10.0

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