{
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  "Package": "rNeighborQTL",
  "Title": "Interval Mapping for Quantitative Trait Loci Underlying Neighbor\nEffects",
  "Version": "1.1.2",
  "Authors@R": "c(\nperson(given = \"Yasuhiro\", family = \"Sato\", role = c(\"aut\", \"cre\"), email = \"sato.yasuhiro.36c@kyoto-u.jp\", comment = c(ORCID = \"0000-0002-6466-723X\")),\nperson(given = \"Kazuya\", family = \"Takeda\", role = \"aut\"),\nperson(given = \"Atsushi J.\", family = \"Nagano\", role = \"aut\", comment = c(ORCID = \"0000-0001-7891-5049\"))\n)",
  "Description": "To enable quantitative trait loci mapping of neighbor\neffects, this package extends a single-marker regression to\ninterval mapping. The theoretical background of the method is\ndescribed in Sato et al. (2021)\n<doi:10.1093/g3journal/jkab017>.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
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  "Maintainer": "Yasuhiro Sato <sato.yasuhiro.36c@kyoto-u.jp>",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-14 05:49:23 UTC",
    "User": "root"
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  "Author": "Yasuhiro Sato [aut, cre]\n(<https://orcid.org/0000-0002-6466-723X>), Kazuya Takeda [aut],\nAtsushi J. Nagano [aut]\n(<https://orcid.org/0000-0001-7891-5049>)",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2021-04-09 04:10:02 UTC",
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    "author": "Yasuhiro Sato <sato.yasuhiro.36c@kyoto-u.jp>",
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    "email": "sato.yasuhiro.36c@kyoto-u.jp",
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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    "calc_pve",
    "eff_neighbor",
    "int_neighbor",
    "min_dist",
    "perm_neighbor",
    "plot_nei",
    "scan_neighbor",
    "sim_nei_qtl"
  ],
  "_help": [
    {
      "page": "calc_neiprob",
      "title": "Calculating a set of neighbor QTL effects from conditional genotype probabilities",
      "topics": [
        "calc_neiprob"
      ]
    },
    {
      "page": "calc_pve",
      "title": "Calculating phenotypic variation explained by neighbor effects",
      "topics": [
        "calc_pve"
      ]
    },
    {
      "page": "decompose_genoprobs",
      "title": "Decomposition of conditional genotype probabilities",
      "topics": [
        "decompose_genoprobs"
      ]
    },
    {
      "page": "eff_neighbor",
      "title": "Estimation of self and neighbor QTL effects across a genome",
      "topics": [
        "eff_neighbor"
      ]
    },
    {
      "page": "genoprobs2selfprobs",
      "title": "Calculating a set of self QTL effects from conditional genotype probabilities",
      "topics": [
        "genoprobs2selfprobs"
      ]
    },
    {
      "page": "get_markers",
      "title": "Reshaping marker information",
      "topics": [
        "get_markers"
      ]
    },
    {
      "page": "int_neighbor",
      "title": "Testing marker-by-marker epistasis in neighbor QTL effects",
      "topics": [
        "int_neighbor"
      ]
    },
    {
      "page": "logLik_glm.fit",
      "title": "Calculating log-likelihood in generalized linear models",
      "topics": [
        "logLik_glm.fit"
      ]
    },
    {
      "page": "min_dist",
      "title": "Calculating the minimum distance",
      "topics": [
        "min_dist"
      ]
    },
    {
      "page": "neiprob",
      "title": "Calculating neighbor QTL effects",
      "topics": [
        "neiprob"
      ]
    },
    {
      "page": "perm_neighbor",
      "title": "Permutation tests for neighbor effects with a QTL model",
      "topics": [
        "perm_neighbor"
      ]
    },
    {
      "page": "plot_eff",
      "title": "Plot self and neighbor QTL effects across a genome",
      "topics": [
        "plot_eff"
      ]
    },
    {
      "page": "plot_nei",
      "title": "Plot LOD score for self or neighbor QTL effects",
      "topics": [
        "plot_nei"
      ]
    },
    {
      "page": "scan_neighbor",
      "title": "Genome scan for neighbor effects with a QTL model",
      "topics": [
        "scan_neighbor"
      ]
    },
    {
      "page": "selfprob",
      "title": "Calculating self QTL effects",
      "topics": [
        "selfprob"
      ]
    },
    {
      "page": "sim_nei_qtl",
      "title": "Phenotype simulation for neighbor QTL effects",
      "topics": [
        "sim_nei_qtl"
      ]
    }
  ],
  "_rundeps": [
    "gaston",
    "lattice",
    "Matrix",
    "qtl",
    "Rcpp",
    "RcppEigen",
    "RcppParallel"
  ],
  "_vignettes": [
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      "source": "rNeighborQTL.Rmd",
      "filename": "rNeighborQTL.html",
      "title": "rNeighborQTL",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Input files",
        "Estimation of QTL effects",
        "LOD score",
        "Extensions",
        "1. Self-genotype effects",
        "2. Composite interval mapping",
        "3. Epistasis in neighbor QTL effects",
        "5. Crossing design",
        "References"
      ],
      "created": "2020-06-04 13:30:07",
      "modified": "2021-04-09 04:10:02",
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