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  "Package": "RepeatABEL",
  "Title": "GWAS for Multiple Observations on Related Individuals",
  "Version": "2.0",
  "Authors@R": "person(\"Lars\", \"Ronnegard\", , \"lars.ronnegard@slu.se\", role = c(\"aut\", \"cre\"))",
  "Description": "Performs genome-wide association studies (GWAS) on\nindividuals that are both related and have repeated\nmeasurements. For each Single Nucleotide Polymorphism (SNP), it\ncomputes score statistic based p-values for a linear mixed\nmodel including random polygenic effects and a random effect\nfor repeated measurements. The computed p-values can be\nvisualized in a Manhattan plot. For more details see Ronnegard\net al. (2016) <doi:10.1111/2041-210X.12535> and for more\nexamples see\n<https://github.com/larsronn/RepeatABEL_Tutorials>.",
  "License": "GPL",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "Collate": "'Compute_GRM2.R' 'Create_gwaa_data2.R' 'Create_gwaa_scan2.R'\n'SmoothSNPmatrix.R' 'chromosome.R' 'constructV.R'\n'estlambda2.R' 'snp.data.R' 'gwaa.data2.R' 'idnames.R'\n'keep_gwaa_data.R' 'map.R' 'nids.R' 'plot.scan.gwaa2.R'\n'preFitModel.R' 'rGLS.R' 'scan.gwaa2.R' 'simulate_PhenData.R'\n'simulate_gendata.R' 'snpnames.R' 'summary_scan_gwaa2.R'",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-27 09:22:11 UTC",
    "User": "root"
  },
  "Author": "Lars Ronnegard [aut, cre]",
  "Maintainer": "Lars Ronnegard <lars.ronnegard@slu.se>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-01-06 11:00:15 UTC",
  "RemoteUrl": "https://github.com/cran/RepeatABEL",
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  "_created": "2026-09-27T09:22:11.000Z",
  "_published": "2026-09-27T09:24:58.260Z",
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  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/36308979109",
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    "author": "Lars Ronnegard <lars.ronnegard@slu.se>",
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    "message": "version 2.0\n",
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    "name": "Lars Ronnegard",
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RepeatABEL"
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    "extra/citation.html",
    "extra/citation.json",
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  "_releases": [
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      "date": "2015-11-24"
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      "date": "2016-08-19"
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  "_exports": [
    "chromosome",
    "compute.GRM",
    "constructV",
    "Create_gwaa_data2",
    "Create_gwaa_scan2",
    "estlambda",
    "idnames",
    "nids",
    "preFitModel",
    "rGLS",
    "simulate_gendata",
    "simulate_PhenData"
  ],
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    {
      "page": "chromosome",
      "title": "Extracts the chromosome numbers",
      "topics": [
        "chromosome"
      ]
    },
    {
      "page": "compute.GRM",
      "title": "Computes a Genetic Relationship Matrix from a GenABEL-like object",
      "topics": [
        "compute.GRM"
      ]
    },
    {
      "page": "constructV",
      "title": "Constructs the (co)variance matrix for y",
      "topics": [
        "constructV"
      ]
    },
    {
      "page": "Create_gwaa_data2",
      "title": "Creates a gwaa.data2 object",
      "topics": [
        "Create_gwaa_data2"
      ]
    },
    {
      "page": "Create_gwaa_scan2",
      "title": "Creates a scan.gwaa2 object",
      "topics": [
        "Create_gwaa_scan2"
      ]
    },
    {
      "page": "estlambda",
      "title": "Function to estimate lambda",
      "topics": [
        "estlambda"
      ]
    },
    {
      "page": "gwaa.data2-class",
      "title": "An S4 class to represent GWAS input data",
      "topics": [
        "gwaa.data2-class"
      ]
    },
    {
      "page": "idnames",
      "title": "Extracts the id names",
      "topics": [
        "idnames"
      ]
    },
    {
      "page": "keep_gwaa_data",
      "title": "A function to subset an gwaa.data2 object",
      "topics": [
        "keep_gwaa_data"
      ]
    },
    {
      "page": "map",
      "title": "Extracts the map information",
      "topics": [
        "map"
      ]
    },
    {
      "page": "nids",
      "title": "Extracts the number of ids",
      "topics": [
        "nids"
      ]
    },
    {
      "page": "plot.scan.gwaa2",
      "title": "Function to plot P-values as a Manhattan plot",
      "topics": [
        "plot.scan.gwaa2"
      ]
    },
    {
      "page": "preFitModel",
      "title": "Fits a linear mixed model (without fixed SNP effects) and computes the fitted variance-covariance matrix for later use in the rGLS function.",
      "topics": [
        "preFitModel"
      ]
    },
    {
      "page": "rGLS",
      "title": "GWAS for Studies having Repeated Measurements on Related Individuals",
      "topics": [
        "rGLS"
      ]
    },
    {
      "page": "scan.gwaa2-class",
      "title": "An S4 class to represent SNP data",
      "topics": [
        "scan.gwaa2-class"
      ]
    },
    {
      "page": "simulate_gendata",
      "title": "Function to simulate genotype data for the RepeatABEL package.",
      "topics": [
        "simulate_gendata"
      ]
    },
    {
      "page": "simulate_PhenData",
      "title": "Simulation function for the RepeatABEL package.",
      "topics": [
        "simulate_PhenData"
      ]
    },
    {
      "page": "SmoothSNPmatrix",
      "title": "Imputes column means to missing genotypes",
      "topics": [
        "SmoothSNPmatrix"
      ]
    },
    {
      "page": "snp.data",
      "title": "An S4 class to represent SNP data",
      "topics": [
        "snp.data"
      ]
    },
    {
      "page": "snpnames",
      "title": "Extracts the snpnames",
      "topics": [
        "snpnames"
      ]
    },
    {
      "page": "summary.scan.gwaa2",
      "title": "Summary function for the rGLS output",
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      ]
    }
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