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  "Title": "Testing Pleiotropy in Multiparental Populations",
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  "Authors@R": "person(given = \"Frederick J\",\nfamily = \"Boehm\",\nrole = c(\"aut\", \"cre\"),\nemail = \"frederick.boehm@gmail.com\",\ncomment = c(ORCID = \"0000-0002-1644-5931\"))",
  "Description": "We implement an adaptation of Jiang & Zeng's (1995)\n<doi:10.1093/genetics/140.3.1111> likelihood ratio test for\ntesting the null hypothesis of pleiotropy against the\nalternative hypothesis, two separate quantitative trait loci.\nThe test differs from that in Jiang & Zeng (1995) and that in\nTian et al. (2016) <doi:10.1534/genetics.115.183624> in that\nour test accommodates multiparental populations.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/fboehm/qtl2pleio",
  "BugReports": "https://github.com/fboehm/qtl2pleio/issues",
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  "Repository": "https://fboehm.r-universe.dev",
  "Date/Publication": "2026-05-29 13:12:10 UTC",
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  "Author": "Frederick J Boehm [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-1644-5931>)",
  "Maintainer": "Frederick J Boehm <frederick.boehm@gmail.com>",
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    "message": "fix: deleted extra parenthesis\n",
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  "_tags": [],
  "_topics": [
    "multiparental-populations",
    "quantitative-genetics",
    "quantitative-trait",
    "cpp"
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    "%>%",
    "add_pmap",
    "boot_pvl",
    "calc_Bhat",
    "calc_covs",
    "calc_lrt_tib",
    "calc_profile_lods",
    "calc_Sigma",
    "check_identical",
    "check_missingness",
    "convert_to_scan1_output",
    "find_pleio_peak_tib",
    "fit1_pvl",
    "get_effects",
    "make_id2keep",
    "plot_pvl",
    "prep_mytab",
    "prep_X_list",
    "rcpp_calc_Bhat",
    "rcpp_calc_Bhat2",
    "rcpp_log_dmvnorm2",
    "scan_multi_onechr",
    "scan_multi_oneqtl",
    "scan_multi_oneqtl_perm",
    "scan_pvl",
    "sim1",
    "subset_input",
    "subset_kinship"
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    {
      "page": "qtl2pleio-package",
      "title": "qtl2pleio.",
      "topics": [
        "qtl2pleio-package",
        "qtl2pleio"
      ]
    },
    {
      "page": "add_pmap",
      "title": "Add physical map contents to tibble",
      "concept": [
        "profile lod tibble functions"
      ],
      "topics": [
        "add_pmap"
      ]
    },
    {
      "page": "boot_pvl",
      "title": "Perform bootstrap sampling and calculate test statistic for each bootstrap sample",
      "topics": [
        "boot_pvl"
      ]
    },
    {
      "page": "calc_Bhat",
      "title": "Calculate estimated allele effects, B matrix",
      "topics": [
        "calc_Bhat"
      ]
    },
    {
      "page": "calc_covs",
      "title": "Calculate Vg and Ve from d-variate phenotype and kinship",
      "topics": [
        "calc_covs"
      ]
    },
    {
      "page": "calc_invsqrt_mat",
      "title": "Calculate matrix inverse square root for a covariance matrix",
      "topics": [
        "calc_invsqrt_mat"
      ]
    },
    {
      "page": "calc_lrt_tib",
      "title": "Calculate a likelihood ratio test statistic from the output of scan_pvl()",
      "topics": [
        "calc_lrt_tib"
      ]
    },
    {
      "page": "calc_profile_lods",
      "title": "Calculate profile lods for all traits",
      "topics": [
        "calc_profile_lods"
      ]
    },
    {
      "page": "calc_Sigma",
      "title": "Calculate the phenotypes covariance matrix Sigma",
      "topics": [
        "calc_Sigma"
      ]
    },
    {
      "page": "calc_sqrt_mat",
      "title": "Calculate matrix square root for a covariance matrix",
      "topics": [
        "calc_sqrt_mat"
      ]
    },
    {
      "page": "check_identical",
      "title": "Check whether a vector, x, has all its entries equal to its first entry",
      "topics": [
        "check_identical"
      ]
    },
    {
      "page": "check_missingness",
      "title": "Check for missingness in phenotypes or covariates",
      "topics": [
        "check_missingness"
      ]
    },
    {
      "page": "convert_to_scan1_output",
      "title": "Convert `scan_multi_oneqtl` output of `qtl2::scan1` output",
      "topics": [
        "convert_to_scan1_output"
      ]
    },
    {
      "page": "find_pleio_peak_tib",
      "title": "Find the marker index corresponding to the peak of the pleiotropy trace in a tibble where the last column contains log likelihood values and the first d columns contain marker ids",
      "topics": [
        "find_pleio_peak_tib"
      ]
    },
    {
      "page": "fit1_pvl",
      "title": "Fit a model for a specified d-tuple of markers",
      "topics": [
        "fit1_pvl"
      ]
    },
    {
      "page": "get_effects",
      "title": "Extract founder allele effects at a single marker from output of qtl2::scan1coef",
      "topics": [
        "get_effects"
      ]
    },
    {
      "page": "make_id2keep",
      "title": "Identify shared subject ids among all inputs: covariates, allele probabilities array, kinship, and phenotypes",
      "topics": [
        "make_id2keep"
      ]
    },
    {
      "page": "plot_pvl",
      "title": "Plot tidied results of a pvl scan",
      "topics": [
        "plot_pvl"
      ]
    },
    {
      "page": "prep_mytab",
      "title": "Prepare mytab object for use within scan_pvl R code",
      "topics": [
        "prep_mytab"
      ]
    },
    {
      "page": "prep_X_list",
      "title": "Create a list of component X matrices for input to stagger_mats, to ultimately create design matrix",
      "topics": [
        "prep_X_list"
      ]
    },
    {
      "page": "process_inputs",
      "title": "Process inputs to scan functions",
      "topics": [
        "process_inputs"
      ]
    },
    {
      "page": "rcpp_calc_Bhat",
      "title": "Estimate allele effects matrix, B hat, with Rcpp functions",
      "topics": [
        "rcpp_calc_Bhat"
      ]
    },
    {
      "page": "rcpp_calc_Bhat2",
      "title": "Estimate allele effects matrix, B hat, with Rcpp functions",
      "topics": [
        "rcpp_calc_Bhat2"
      ]
    },
    {
      "page": "rcpp_log_dmvnorm2",
      "title": "Calculate log likelihood for a multivariate normal",
      "topics": [
        "rcpp_log_dmvnorm2"
      ]
    },
    {
      "page": "scan_multi_onechr",
      "title": "Perform multivariate, one-QTL model fitting for markers on one chromosome",
      "topics": [
        "scan_multi_onechr"
      ]
    },
    {
      "page": "scan_multi_oneqtl",
      "title": "Perform multivariate, one-QTL model fitting for markers on all chromosomes",
      "topics": [
        "scan_multi_oneqtl"
      ]
    },
    {
      "page": "scan_multi_oneqtl_perm",
      "title": "Permute the phenotypes matrix and then scan the genome. Record the genomewide greatest LOD score for each permuted data set.",
      "topics": [
        "scan_multi_oneqtl_perm"
      ]
    },
    {
      "page": "scan_pvl",
      "title": "Perform model fitting for all ordered pairs of markers in a genomic region of interest",
      "topics": [
        "scan_pvl"
      ]
    },
    {
      "page": "sim1",
      "title": "Simulate a single multivariate data set consisting of n subjects and d phenotypes for each",
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        "sim1"
      ]
    },
    {
      "page": "subset_input",
      "title": "Subset an input object - allele probabilities array or phenotypes matrix or covariates matrix. Kinship has its own subset function",
      "topics": [
        "subset_input"
      ]
    },
    {
      "page": "subset_kinship",
      "title": "Subset a kinship matrix to include only those subjects present in all inputs",
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        "subset_kinship"
      ]
    }
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