Package: switchBox 1.49.0

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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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
switchBox/json (API)

# Install 'switchBox' in R:

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

Datasets:

matTesting - Gene expression matrix for test set data
matTraining - Gene expression matrix for training set data
testingGroup - Testing set phenotypes
trainingGroup - Training set phenotypes

On BioConductor:switchBox-1.49.0(bioc 3.24)switchBox-1.48.0(bioc 3.23)

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

software statisticalmethod classification

5.23 score 1 packages 94 scripts 3 mentions 30 exports 7 dependencies

Last updated from:aafbb00397. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	145
linux-devel-arm64	WARNING	132
linux-devel-x86_64	WARNING	201
source / vignettes	OK	168
linux-release-arm64	WARNING	155
linux-release-x86_64	WARNING	190
macos-release-arm64	WARNING	118
macos-release-x86_64	WARNING	157
macos-oldrel-arm64	WARNING	81
macos-oldrel-x86_64	WARNING	325
windows-devel	WARNING	105
windows-release	WARNING	114
windows-oldrel	WARNING	135
wasm-release	OK	142

Exports:KTSP.Classify KTSP.Train SWAP.Calculate.BasicTSPScores SWAP.Calculate.SignedTSPScores SWAP.CalculateScores SWAP.CalculateSignedScore SWAP.Filter.Wilcoxon SWAP.GetKFoldIndices SWAP.GetKTSP.PredictionStats SWAP.GetKTSP.Result SWAP.GetKTSP.TrainTestResults SWAP.Kby.Measurement SWAP.Kby.Ttest SWAP.KTSP.Classify SWAP.KTSP.CV SWAP.KTSP.LOO SWAP.KTSP.Statistics SWAP.KTSP.Train SWAP.MakeTrainTestData SWAP.MakeTSPTable SWAP.PlotKTSP.GenePairBoxplot SWAP.PlotKTSP.GenePairClassesBoxplot SWAP.PlotKTSP.GenePairScatter SWAP.PlotKTSP.Genes SWAP.PlotKTSP.TrainTestROC SWAP.PlotKTSP.Votes SWAP.ScoreMatrixToVector SWAP.ScoreVectorToMatrix SWAP.Train.1TSP SWAP.Train.KTSP

Dependencies:bitops caTools gplots gtools KernSmooth pROC Rcpp

Working with the switchBox package

Rendered fromswitchBox.Rnwusingutils::Sweave

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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 data	matTesting
Gene expression matrix for training set data	matTraining
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 phenotype	SWAP.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 phenotypes	testingGroup
Training set phenotypes	trainingGroup