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  "Title": "Visualize and Parse the Output of 'BeXY'",
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  "Maintainer": "Madleina Caduff <madleina.caduff@unifr.ch>",
  "Description": "Provides functions for summarizing and plotting the output\nof the command-line tool 'BeXY'\n(<https://bitbucket.org/wegmannlab/bexy>), a tool that performs\nBayesian inference of sex chromosome karyotypes and sex-linked\nscaffolds from low-depth sequencing data.",
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    "User": "root"
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  "Author": "Madleina Caduff [aut, cre], Raphael Eckel [ctb], Christoph\nLeuenberger [ctb], Daniel Wegmann [aut]",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2024-08-24 02:46:56 UTC",
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    "extra/citation.cff",
    "extra/citation.html",
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    "extra/contents.json",
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      "date": "2024-08-26"
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    "bexy",
    "getPosteriorMeanRho",
    "getPosteriorModeAutosomalTrisomy",
    "getPosteriorModeScaffoldTypes",
    "getPosteriorModeSexKaryotypes",
    "getSamplesWithAutosomalTrisomy",
    "getSamplesWithThisKaryotype",
    "getScaffoldsWithThisType",
    "plot.bexy",
    "plotAutosomalTrisomy",
    "plotAutosomalTrisomyCounts",
    "plotAutosomalTrisomyPosteriorProbabilities",
    "plotBars",
    "plotCounts",
    "plotMCMCTrace",
    "plotTernary",
    "print.bexy",
    "summary.bexy",
    "writePosteriorModeAutosomalTrisomies",
    "writePosteriorModeScaffoldTypes",
    "writePosteriorModeSexKaryotypes"
  ],
  "_help": [
    {
      "page": "bexy",
      "title": "Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data",
      "topics": [
        "bexy"
      ]
    },
    {
      "page": "getPosteriorMeanRho",
      "title": "Getting posterior mean rho (ploidy ratio parameter) for each scaffold",
      "topics": [
        "getPosteriorMeanRho"
      ]
    },
    {
      "page": "getPosteriorModeAutosomalTrisomy",
      "title": "Getting the posterior mode for each autosomal trisomy",
      "topics": [
        "getPosteriorModeAutosomalTrisomy"
      ]
    },
    {
      "page": "getPosteriorModeScaffoldTypes",
      "title": "Getting the posterior mode for each scaffold type",
      "topics": [
        "getPosteriorModeScaffoldTypes"
      ]
    },
    {
      "page": "getPosteriorModeSexKaryotypes",
      "title": "Getting the posterior mode for each sex karyotype",
      "topics": [
        "getPosteriorModeSexKaryotypes"
      ]
    },
    {
      "page": "getSamplesWithAutosomalTrisomy",
      "title": "Getting all samples classified as a certain autosomal trisomy",
      "topics": [
        "getSamplesWithAutosomalTrisomy"
      ]
    },
    {
      "page": "getSamplesWithThisKaryotype",
      "title": "Getting all samples classified as a specific sex karyotype",
      "topics": [
        "getSamplesWithThisKaryotype"
      ]
    },
    {
      "page": "getScaffoldsWithThisType",
      "title": "Getting all scaffolds classified as a specific scaffold type",
      "topics": [
        "getScaffoldsWithThisType"
      ]
    },
    {
      "page": "plot.bexy",
      "title": "Plotting a bexy object. To customize the plots, please call the respective plotting functions directly (e.g. plotTernary, plotCounts, plotBars...).",
      "topics": [
        "plot.bexy"
      ]
    },
    {
      "page": "plotAutosomalTrisomy",
      "title": "Plotting the autosomal trisomies",
      "topics": [
        "plotAutosomalTrisomy"
      ]
    },
    {
      "page": "plotAutosomalTrisomyCounts",
      "title": "Plotting the autosomal trisomies: counts on that scaffold",
      "topics": [
        "plotAutosomalTrisomyCounts"
      ]
    },
    {
      "page": "plotAutosomalTrisomyPosteriorProbabilities",
      "title": "Plotting the autosomal trisomies: posterior probabilities",
      "topics": [
        "plotAutosomalTrisomyPosteriorProbabilities"
      ]
    },
    {
      "page": "plotBars",
      "title": "Plotting a barplot with the posterior probabilities of each sex karyotype per sample",
      "topics": [
        "plotBars"
      ]
    },
    {
      "page": "plotCounts",
      "title": "Plotting the percentage of counts mapping to two scaffolds (by default a Y-linked scaffold against a X-linked scaffold), colored by sex karyotype",
      "topics": [
        "plotCounts"
      ]
    },
    {
      "page": "plotMCMCTrace",
      "title": "Plot the MCMC trace for a specific parameter",
      "topics": [
        "plotMCMCTrace"
      ]
    },
    {
      "page": "plotTernary",
      "title": "Plotting the ternary of a bexy object",
      "topics": [
        "plotTernary"
      ]
    },
    {
      "page": "print.bexy",
      "title": "Printing a bexy object",
      "topics": [
        "print.bexy"
      ]
    },
    {
      "page": "summary.bexy",
      "title": "Summarizing a bexy object",
      "topics": [
        "summary.bexy"
      ]
    },
    {
      "page": "writePosteriorModeAutosomalTrisomies",
      "title": "Write a file with the posterior mode for each autosomal trisomy",
      "topics": [
        "writePosteriorModeAutosomalTrisomies"
      ]
    },
    {
      "page": "writePosteriorModeScaffoldTypes",
      "title": "Write a file with the posterior mode for each scaffold type",
      "topics": [
        "writePosteriorModeScaffoldTypes"
      ]
    },
    {
      "page": "writePosteriorModeSexKaryotypes",
      "title": "Write a file with the posterior mode for each sex karyotype",
      "topics": [
        "writePosteriorModeSexKaryotypes"
      ]
    }
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