{
  "_id": "6ae32f7195ca2370cc8ce033",
  "Package": "switchBox",
  "Version": "1.49.0",
  "Date": "2016-10-03",
  "Title": "Utilities to train and validate classifiers based on pair\nswitching using the K-Top-Scoring-Pair (KTSP) algorithm",
  "Author": "Bahman Afsari <bahman@jhu.edu>, Luigi Marchionni\n<marchion@jhu.edu>, Wikum Dinalankara <wdinala1@jhmi.edu>",
  "Maintainer": "Bahman Afsari <bahman@jhu.edu>, Luigi Marchionni\n<marchion@jhu.edu>, Wikum Dinalankara <wdinala1@jhmi.edu>",
  "Description": "The package offer different classifiers based on\ncomparisons of pair of features (TSP), using various decision\nrules (e.g., majority wins principle).",
  "biocViews": "Software, StatisticalMethod, Classification",
  "License": "GPL-2",
  "Packaged": {
    "Date": "2026-10-29 10:45:55 UTC",
    "User": "root"
  },
  "NeedsCompilation": "yes",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:39:40 UTC",
  "RemoteUrl": "https://github.com/bioc/switchBox",
  "RemoteRef": "HEAD",
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  "_created": "2026-10-29T10:45:55.000Z",
  "_published": "2026-10-29T11:35:12.860Z",
  "_upstream": "https://github.com/bioc/switchBox",
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    "email": "bahman@jhu.edu",
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    "description": "",
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    "SWAP.PlotKTSP.GenePairClassesBoxplot",
    "SWAP.PlotKTSP.GenePairScatter",
    "SWAP.PlotKTSP.Genes",
    "SWAP.PlotKTSP.TrainTestROC",
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    "SWAP.ScoreVectorToMatrix",
    "SWAP.Train.1TSP",
    "SWAP.Train.KTSP"
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  "_help": [
    {
      "page": "switchBox-package",
      "title": "A package to train and apply K-Top-Scoring-Pair (KTSP) classifiers.",
      "topics": [
        "switchBox-package",
        "switchBox"
      ]
    },
    {
      "page": "KTSP.Classify",
      "title": "Function to classify samples using a KTSP classifier.",
      "topics": [
        "KTSP.Classify"
      ]
    },
    {
      "page": "KTSP.Train",
      "title": "Funtion for training the K-TSP classifier.",
      "topics": [
        "KTSP.Train"
      ]
    },
    {
      "page": "matTesting",
      "title": "Gene expression matrix for test set data",
      "topics": [
        "matTesting"
      ]
    },
    {
      "page": "matTraining",
      "title": "Gene expression matrix for training set data",
      "topics": [
        "matTraining"
      ]
    },
    {
      "page": "SWAP.Calculate.BasicTSPScores",
      "title": "Function to calculate basic TSP scores.",
      "topics": [
        "SWAP.Calculate.BasicTSPScores"
      ]
    },
    {
      "page": "SWAP.Calculate.SignedTSPScores",
      "title": "Function to calculate signed TSP scores.",
      "topics": [
        "SWAP.Calculate.SignedTSPScores"
      ]
    },
    {
      "page": "SWAP.CalculateScores",
      "title": "Function to calculate the pair-wise scores with any given score function.",
      "topics": [
        "SWAP.CalculateScores"
      ]
    },
    {
      "page": "SWAP.CalculateSignedScore",
      "title": "Function to calculate the pair-wise scores.",
      "topics": [
        "SWAP.CalculateSignedScore"
      ]
    },
    {
      "page": "SWAP.Filter.Wilcoxon",
      "title": "Statistical feature filtering based on Wilcoxon test on the ranks of expressions.",
      "topics": [
        "SWAP.Filter.Wilcoxon"
      ]
    },
    {
      "page": "SWAP.GetKTSP.PredictionStats",
      "title": "Function for computing various performance measures related to prediction.",
      "topics": [
        "SWAP.GetKTSP.PredictionStats"
      ]
    },
    {
      "page": "SWAP.GetKTSP.Result",
      "title": "Function for prediction followed by computing various performance measures related to prediction.",
      "topics": [
        "SWAP.GetKTSP.Result"
      ]
    },
    {
      "page": "SWAP.GetKTSP.TrainTestResults",
      "title": "Trains a kTSP on given training data and provides performance on testing data.",
      "topics": [
        "SWAP.GetKTSP.TrainTestResults"
      ]
    },
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      "page": "SWAP.Kby.Measurement",
      "title": "K selection for a kTSP classifier.",
      "topics": [
        "SWAP.Kby.Measurement"
      ]
    },
    {
      "page": "SWAP.Kby.Ttest",
      "title": "K selection for a kTSP classifier.",
      "topics": [
        "SWAP.Kby.Ttest"
      ]
    },
    {
      "page": "SWAP.KTSP.Classify",
      "title": "Function to classify samples using a KTSP classifier.",
      "topics": [
        "SWAP.KTSP.Classify"
      ]
    },
    {
      "page": "SWAP.KTSP.CV",
      "title": "Performs k-fold cross validation.",
      "topics": [
        "SWAP.KTSP.CV"
      ]
    },
    {
      "page": "SWAP.KTSP.LOO",
      "title": "Performs leave one out cross validation.",
      "topics": [
        "SWAP.KTSP.LOO"
      ]
    },
    {
      "page": "SWAP.KTSP.Statistic",
      "title": "Function computing TSP votes (comparisons) and combine their votes. The default is the kTSP statistics, sum of the votes.",
      "topics": [
        "SWAP.KTSP.Statistics"
      ]
    },
    {
      "page": "SWAP.KTSP.Train",
      "title": "Deprecated function for training the K-TSP classifier.",
      "topics": [
        "SWAP.KTSP.Train"
      ]
    },
    {
      "page": "SWAP.MakeTSPTable",
      "title": "Make a table of TSPs in order of TSP score.",
      "topics": [
        "SWAP.MakeTSPTable"
      ]
    },
    {
      "page": "SWAP.PlotKTSP.GenePairBoxplot",
      "title": "Plots a feature pair as boxplots.",
      "topics": [
        "SWAP.PlotKTSP.GenePairBoxplot"
      ]
    },
    {
      "page": "SWAP.PlotKTSP.GenePairClassesBoxplot",
      "title": "Plots a feature pair as seperated by class as boxplots.",
      "topics": [
        "SWAP.PlotKTSP.GenePairClassesBoxplot"
      ]
    },
    {
      "page": "SWAP.PlotKTSP.GenePairScatter",
      "title": "Make a scatter plot of two features.",
      "topics": [
        "SWAP.PlotKTSP.GenePairScatter"
      ]
    },
    {
      "page": "SWAP.PlotKTSP.Genes",
      "title": "Plot features seperated by phenotype",
      "topics": [
        "SWAP.PlotKTSP.Genes"
      ]
    },
    {
      "page": "SWAP.PlotKTSP.TrainTestROC",
      "title": "Plots an ROC curve for training and testing results.",
      "topics": [
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      ]
    },
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      "page": "SWAP.PlotKTSP.Votes",
      "title": "Plots a heatmap of k-TSP votes.",
      "topics": [
        "SWAP.PlotKTSP.Votes"
      ]
    },
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      "page": "SWAP.Train.1TSP",
      "title": "Function for training the 1-TSP classifier.",
      "topics": [
        "SWAP.Train.1TSP"
      ]
    },
    {
      "page": "SWAP.Train.KTSP",
      "title": "Function for training the K-TSP classifier.",
      "topics": [
        "SWAP.Train.KTSP"
      ]
    },
    {
      "page": "testingGroup",
      "title": "Testing set phenotypes",
      "topics": [
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    },
    {
      "page": "trainingGroup",
      "title": "Training set phenotypes",
      "topics": [
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      "source": "switchBox.Rnw",
      "filename": "switchBox.pdf",
      "title": "Working with the switchBox package",
      "engine": "utils::Sweave",
      "headings": [
        " Introduction ",
        " Installing the package ",
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        "Training KTSP algorithm",
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        "Compute the signed TSP scores",
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        " Literature Cited "
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      "modified": "2018-11-16 13:46:25",
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