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  "Date": "2025-12-14",
  "Title": "Bayesian QTL Mapping Toolkit",
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  "Author": "Charles C. Berry [aut, cre]",
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  "Description": "QTL mapping toolkit for inbred crosses and recombinant\ninbred lines. Includes maximum likelihood and Bayesian tools.",
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      "title": "Some Introductory Comments",
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    {
      "page": "bqtl",
      "title": "Bayesian QTL Model Fitting",
      "topics": [
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    {
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      "title": "Internal BQTL functions",
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        "map.dx",
        "rhs.bqtl",
        "uniq.config",
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    {
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      "title": "Get loglikelihoods for many models of a common form",
      "topics": [
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    {
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      "title": "Extract Coefficients from fitted objects",
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        "coef.bqtl.list"
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      "topics": [
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      "page": "formula.bqtl",
      "title": "Extract formula from bqtl object",
      "topics": [
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    {
      "page": "lapadj",
      "title": "Approximate marginal posterior for chosen model",
      "topics": [
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    {
      "page": "linear.bayes",
      "title": "Bayesian QTL mapping via Linearized Likelihood",
      "topics": [
        "linear.bayes"
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    },
    {
      "page": "little.ana.bc",
      "title": "A simulated dataset",
      "topics": [
        "little.ana.bc"
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    },
    {
      "page": "little.ana.f2",
      "title": "A simulated dataset",
      "topics": [
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      "page": "little.bc.markers",
      "title": "Simulated Marker Data",
      "topics": [
        "little.bc.markers"
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    {
      "page": "little.bc.pheno",
      "title": "Simulated Phenotype Data",
      "topics": [
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    },
    {
      "page": "little.f2.markers",
      "title": "Simulated Marker Data",
      "topics": [
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    {
      "page": "little.f2.pheno",
      "title": "Simulated Phenotype Data",
      "topics": [
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      "page": "little.dx",
      "title": "Marker Map Description for Simulated Data",
      "topics": [
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    },
    {
      "page": "little.map.frame",
      "title": "Package of Simulated Marker Map Information",
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    {
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      "title": "Package of Simulated Marker Map Information",
      "topics": [
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      "page": "locus",
      "title": "Lookup loci or effects for genetic model formulas",
      "topics": [
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        "dom",
        "locus"
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    },
    {
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      "title": "Extract loglikelihood, log posterior, or posterior from fitted models",
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        "loglik.bqtl",
        "loglik.bqtl.list",
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        "logpost",
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        "posterior.bqtl.list",
        "posterior.default"
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    {
      "page": "make.analysis.obj",
      "title": "Set up data for QTL mapping",
      "topics": [
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    {
      "page": "make.loc.right",
      "title": "Keep track of fully informative markers or states",
      "topics": [
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    {
      "page": "make.location.prior",
      "title": "Provide a default prior",
      "topics": [
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    },
    {
      "page": "make.map.frame",
      "title": "Create marker map specifications",
      "topics": [
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    },
    {
      "page": "make.marker.numeric",
      "title": "Translate a marker.frame.object to numeric matrix",
      "topics": [
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    {
      "page": "make.regressor.matrix",
      "title": "Create regressors using expected marker values",
      "topics": [
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    {
      "page": "make.state.matrix",
      "title": "Create state.matrix.object",
      "topics": [
        "make.state.matrix"
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    {
      "page": "make.varcov",
      "title": "Create moment matrices",
      "topics": [
        "make.varcov"
      ]
    },
    {
      "page": "map.index",
      "title": "Look up numerical index(es) of map locations",
      "topics": [
        "map.index",
        "map.index.analysis.object",
        "map.index.default"
      ]
    },
    {
      "page": "map.location",
      "title": "Report map location",
      "topics": [
        "map.loc",
        "map.location",
        "map.location.analysis.object",
        "map.location.bqtl",
        "map.location.bqtl.list",
        "map.location.default"
      ]
    },
    {
      "page": "map.names",
      "title": "Look up names of markers or loci",
      "topics": [
        "map.names",
        "map.names.analysis.object",
        "map.names.bqtl",
        "map.names.bqtl.list",
        "map.names.default",
        "map.names.map.frame"
      ]
    },
    {
      "page": "marker.fill",
      "title": "Map Positions Between Markers",
      "topics": [
        "marker.fill"
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    },
    {
      "page": "marker.levels",
      "title": "Define marker level codes",
      "topics": [
        "bc1.levels",
        "f2.levels",
        "marker.levels",
        "ri.levels"
      ]
    },
    {
      "page": "plot.map.frame",
      "title": "plots by chromosome location",
      "topics": [
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        "plot.map.frame"
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    },
    {
      "page": "predict.bqtl",
      "title": "fitted values from QTL models",
      "topics": [
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        "predict.bqtl"
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    },
    {
      "page": "predict.linear.bayes",
      "title": "Residuals or Predicted Values for linear.bayes objects",
      "topics": [
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        "predict.linear.bayes",
        "residuals.linear.bayes"
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    },
    {
      "page": "residuals.bqtl",
      "title": "Residuals from QTL models",
      "topics": [
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    {
      "page": "summary.adj",
      "title": "Summarize Laplace approximations",
      "topics": [
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    },
    {
      "page": "summary.bqtl",
      "title": "Summarize bqtl object",
      "topics": [
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    },
    {
      "page": "summary.map.frame",
      "title": "Summary methods for basic data objects",
      "topics": [
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    {
      "page": "summary.swap",
      "title": "Summarize Gibbs samples for a k-gene model",
      "topics": [
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    },
    {
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