Package: switchBox 1.41.0

Bahman Afsari

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).

Authors:Bahman Afsari <[email protected]>, Luigi Marchionni <[email protected]>, Wikum Dinalankara <[email protected]>

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switchBox.pdf |switchBox.html✨
switchBox/json (API)

# Install 'switchBox' in R:
install.packages('switchBox', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On BioConductor:switchBox-1.41.0(bioc 3.20)switchBox-1.40.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

30 exports 1.16 score 8 dependencies 1 dependents 3 mentions

Last updated 2 months agofrom:857b4afc6c

Exports:KTSP.ClassifyKTSP.TrainSWAP.Calculate.BasicTSPScoresSWAP.Calculate.SignedTSPScoresSWAP.CalculateScoresSWAP.CalculateSignedScoreSWAP.Filter.WilcoxonSWAP.GetKFoldIndicesSWAP.GetKTSP.PredictionStatsSWAP.GetKTSP.ResultSWAP.GetKTSP.TrainTestResultsSWAP.Kby.MeasurementSWAP.Kby.TtestSWAP.KTSP.ClassifySWAP.KTSP.CVSWAP.KTSP.LOOSWAP.KTSP.StatisticsSWAP.KTSP.TrainSWAP.MakeTrainTestDataSWAP.MakeTSPTableSWAP.PlotKTSP.GenePairBoxplotSWAP.PlotKTSP.GenePairClassesBoxplotSWAP.PlotKTSP.GenePairScatterSWAP.PlotKTSP.GenesSWAP.PlotKTSP.TrainTestROCSWAP.PlotKTSP.VotesSWAP.ScoreMatrixToVectorSWAP.ScoreVectorToMatrixSWAP.Train.1TSPSWAP.Train.KTSP

Dependencies:bitopscaToolsgplotsgtoolsKernSmoothplyrpROCRcpp

Working with the switchBox package

Rendered fromswitchBox.Rnwusingutils::Sweaveon Jun 30 2024.

Last update: 2018-11-16
Started: 2014-09-05

Readme and manuals

Help Manual

Help pageTopics
A package to train and apply K-Top-Scoring-Pair (KTSP) classifiers.switchBox-package switchBox
Function to classify samples using a KTSP classifier.KTSP.Classify
Funtion for training the K-TSP classifier.KTSP.Train
Gene expression matrix for test set datamatTesting
Gene expression matrix for training set datamatTraining
Function to calculate basic TSP scores.SWAP.Calculate.BasicTSPScores
Function to calculate signed TSP scores.SWAP.Calculate.SignedTSPScores
Function to calculate the pair-wise scores with any given score function.SWAP.CalculateScores
Function to calculate the pair-wise scores.SWAP.CalculateSignedScore
Statistical feature filtering based on Wilcoxon test on the ranks of expressions.SWAP.Filter.Wilcoxon
Function for computing various performance measures related to prediction.SWAP.GetKTSP.PredictionStats
Function for prediction followed by computing various performance measures related to prediction.SWAP.GetKTSP.Result
Trains a kTSP on given training data and provides performance on testing data.SWAP.GetKTSP.TrainTestResults
K selection for a kTSP classifier.SWAP.Kby.Measurement
K selection for a kTSP classifier.SWAP.Kby.Ttest
Function to classify samples using a KTSP classifier.SWAP.KTSP.Classify
Performs k-fold cross validation.SWAP.KTSP.CV
Performs leave one out cross validation.SWAP.KTSP.LOO
Function computing TSP votes (comparisons) and combine their votes. The default is the kTSP statistics, sum of the votes.SWAP.KTSP.Statistics
Deprecated function for training the K-TSP classifier.SWAP.KTSP.Train
Make a table of TSPs in order of TSP score.SWAP.MakeTSPTable
Plots a feature pair as boxplots.SWAP.PlotKTSP.GenePairBoxplot
Plots a feature pair as seperated by class as boxplots.SWAP.PlotKTSP.GenePairClassesBoxplot
Make a scatter plot of two features.SWAP.PlotKTSP.GenePairScatter
Plot features seperated by phenotypeSWAP.PlotKTSP.Genes
Plots an ROC curve for training and testing results.SWAP.PlotKTSP.TrainTestROC
Plots a heatmap of k-TSP votes.SWAP.PlotKTSP.Votes
Function for training the 1-TSP classifier.SWAP.Train.1TSP
Function for training the K-TSP classifier.SWAP.Train.KTSP
Testing set phenotypestestingGroup
Training set phenotypestrainingGroup