{
  "_id": "6ad1d224d3c80a766859c0ba",
  "Package": "statgenQTLxT",
  "Type": "Package",
  "Title": "Multi-Trait and Multi-Trial Genome Wide Association Studies",
  "Version": "1.0.3",
  "Date": "2025-07-23",
  "Authors@R": "c(person(given = \"Bart-Jan\", \nfamily = \"van Rossum\",\nemail = \"bart-jan.vanrossum@wur.nl\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-8673-2514\")),\nperson(given = \"Willem\",\nfamily = \"Kruijer\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0001-7179-1733\")),\nperson(given = \"Fred\",\nfamily = \"van Eeuwijk\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0003-3672-2921\")),\nperson(given = \"Martin P\",\nfamily = \"Boer\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-1879-4588\")),\nperson(given = \"Daniela\",\nfamily = \"Bustos-Korts\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0003-3827-6726\")),\nperson(given = \"Emilie J\",\nfamily = \"Millet\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-2913-4892\")),\nperson(given = \"Joao\",\nfamily = \"Paulo\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-4180-0763\")),\nperson(given = \"Maikel\",\nfamily = \"Verouden\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-4893-3323\")),\nperson(given = \"Ron\",\nfamily = \"Wehrens\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-8798-5599\")),\nperson(given = \"Choazhi\",\nfamily = \"Zheng\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0001-6030-3933\"))\n)",
  "Description": "Fast multi-trait and multi-trail Genome Wide Association\nStudies (GWAS) following the method described in Zhou and\nStephens. (2014), <doi:10.1038/nmeth.2848>. One of a series of\nstatistical genetic packages for streamlining the analysis of\ntypical plant breeding experiments developed by Biometris.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "LazyData": "true",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-16 07:09:36 UTC",
    "User": "root"
  },
  "Author": "Bart-Jan van Rossum [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-8673-2514>), Willem Kruijer [aut]\n(ORCID: <https://orcid.org/0000-0001-7179-1733>), Fred van\nEeuwijk [ctb] (ORCID: <https://orcid.org/0000-0003-3672-2921>),\nMartin P Boer [ctb] (ORCID:\n<https://orcid.org/0000-0002-1879-4588>), Daniela Bustos-Korts\n[ctb] (ORCID: <https://orcid.org/0000-0003-3827-6726>), Emilie\nJ Millet [ctb] (ORCID:\n<https://orcid.org/0000-0002-2913-4892>), Joao Paulo [ctb]\n(ORCID: <https://orcid.org/0000-0002-4180-0763>), Maikel\nVerouden [ctb] (ORCID:\n<https://orcid.org/0000-0002-4893-3323>), Ron Wehrens [ctb]\n(ORCID: <https://orcid.org/0000-0002-8798-5599>), Choazhi Zheng\n[ctb] (ORCID: <https://orcid.org/0000-0001-6030-3933>)",
  "Maintainer": "Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>",
  "Repository": "https://bartjanvanrossum.r-universe.dev",
  "Date/Publication": "2025-07-23 08:50:02 UTC",
  "RemoteUrl": "https://github.com/cran/statgenQTLxT",
  "RemoteRef": "HEAD",
  "RemoteSha": "e8a8806b23aea5b25acac97c61ac5733df4fe301",
  "_user": "bartjanvanrossum",
  "_type": "src",
  "_file": "statgenQTLxT_1.0.3.tar.gz",
  "_fileid": "https://r2.ropensci.org/4eaa29c00dcf3e3fad1bd47860977f2d46061143d9fce337ff0f49b4d374e61f",
  "_filesize": 1322548,
  "_sha256": "4eaa29c00dcf3e3fad1bd47860977f2d46061143d9fce337ff0f49b4d374e61f",
  "_expires": "2027-01-24T07:28:34.000Z",
  "_created": "2026-10-16T07:09:36.000Z",
  "_published": "2026-10-16T07:28:35.939Z",
  "_buildurl": "https://github.com/r-universe/bartjanvanrossum/actions/runs/38865052648",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 116857367756,
      "time": 151,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12030803099"
    },
    {
      "job": 116857367725,
      "time": 153,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12030668988"
    },
    {
      "job": 116857367856,
      "time": 146,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12031540406"
    },
    {
      "job": 116857367621,
      "time": 157,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12030669000"
    },
    {
      "job": 116857367726,
      "time": 144,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12032001353"
    },
    {
      "job": 116857367581,
      "time": 286,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12031651314"
    },
    {
      "job": 116857367656,
      "time": 144,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12030948224"
    },
    {
      "job": 116857367622,
      "time": 301,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12031821130"
    },
    {
      "job": 116855916735,
      "time": 259,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12031335415"
    },
    {
      "job": 116857367682,
      "time": 126,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12030144901"
    },
    {
      "job": 116857367816,
      "time": 401,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12030744321"
    },
    {
      "job": 116857368438,
      "time": 186,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12030946619"
    },
    {
      "job": 116857367799,
      "time": 148,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12031505482"
    },
    {
      "job": 116857367662,
      "time": 401,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12030704288"
    },
    {
      "job": 116857367896,
      "time": 101,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12031435570"
    }
  ],
  "_upstream": "https://github.com/cran/statgenQTLxT",
  "_commit": {
    "id": "e8a8806b23aea5b25acac97c61ac5733df4fe301",
    "author": "Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.0.3\n",
    "time": 1753260602
  },
  "_maintainer": {
    "name": "Bart-Jan van Rossum",
    "email": "bart-jan.vanrossum@wur.nl",
    "login": "bartjanvanrossum",
    "description": "",
    "uuid": 28725410,
    "orcid": "0000-0002-8673-2514"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "sommer",
      "version": ">= 4.2.0",
      "role": "Imports"
    },
    {
      "package": "statgenGWAS",
      "version": ">= 1.0.9",
      "role": "Imports"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "tinytest",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "bartjanvanrossum",
      "count": 4,
      "uuid": 28725410
    }
  ],
  "_userbio": {
    "uuid": 28725410,
    "type": "user",
    "name": "Bart-Jan van Rossum",
    "followers": 4
  },
  "_downloads": {
    "count": 266,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/statgenQTLxT"
  },
  "_searchresults": 3,
  "_topics": [
    "openblas",
    "cpp",
    "openmp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/statgenQTLxT.html"
  ],
  "_realowner": "bartjanvanrossum",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2023-02-23"
    },
    {
      "version": "1.0.1",
      "date": "2023-04-04"
    },
    {
      "version": "1.0.2",
      "date": "2024-01-23"
    },
    {
      "version": "1.0.3",
      "date": "2025-07-23"
    }
  ],
  "_exports": [
    "runMultiTraitGwas"
  ],
  "_datasets": [
    {
      "name": "gDataDropsRestr",
      "title": "Subset of DROPS data for use in examples",
      "object": "gDataDropsRestr",
      "class": [
        "gData"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "gDataDropsRestr",
      "title": "Subset of DROPS data for use in examples",
      "topics": [
        "gDataDropsRestr"
      ]
    },
    {
      "page": "runMultiTraitGwas",
      "title": "Perform multi-trait GWAS",
      "topics": [
        "runMultiTraitGwas"
      ]
    }
  ],
  "_readme": "https://github.com/cran/statgenQTLxT/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "data.table",
    "dotCall64",
    "enhancer",
    "farver",
    "foreach",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "iterators",
    "labeling",
    "lattice",
    "lifecycle",
    "LMMsolver",
    "MASS",
    "Matrix",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RcppProgress",
    "rlang",
    "S7",
    "scales",
    "sommer",
    "spam",
    "statgenGWAS",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_vignettes": [
    {
      "source": "statgenQTLxT.Rmd",
      "filename": "statgenQTLxT.html",
      "title": "Multi-trait GWAS with the statgenQTLxT package",
      "author": "Bart-Jan van Rossum",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Multi-Trait GWAS",
        "Theoretical background",
        "Hypotheses for the SNP-effects",
        "Models for the genetic and residual covariance",
        "The class gData",
        "Worked example 1: multiple traits in one trial",
        "Create gData object",
        "Recoding and cleaning of markers",
        "Running Multi-trait GWAS",
        "GWAS Summary",
        "GWAS Plots",
        "QQ plots",
        "Manhattan plots",
        "QTL plots",
        "Kinship matrices",
        "Worked example 2: one trait measured in multiple trials",
        "Multi-trial GWAS",
        "Further options",
        "Significance thresholds",
        "Variance components",
        "Covariates",
        "Minor Allele Frequency",
        "Estimation of common SNP effects and QTL×E effects.",
        "References"
      ],
      "created": "2023-02-23 08:40:03",
      "modified": "2023-02-23 08:40:03",
      "commits": 1
    }
  ],
  "_score": 2.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "statgenqtlxt",
  "_universes": [
    "bartjanvanrossum"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-10-16T07:12:10.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "e8a8806b23aea5b25acac97c61ac5733df4fe301",
      "fileid": "https://r2.ropensci.org/c6d97417c72ff4f250cc562aa9d00b91dbe4dfd4b3a9ff5670cf234aa4e3112e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bartjanvanrossum/actions/runs/38865052648"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-10-16T07:12:04.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "e8a8806b23aea5b25acac97c61ac5733df4fe301",
      "fileid": "https://r2.ropensci.org/42a3736a5a3884171939d25488ab45930de0ed26b7dc2e7d73ba3989ae3be99d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bartjanvanrossum/actions/runs/38865052648"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-10-16T07:12:09.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "e8a8806b23aea5b25acac97c61ac5733df4fe301",
      "fileid": "https://r2.ropensci.org/6a4fedbb92f66d63bfc627be33ef8825b3153392754f8cecc79df1b55d94342e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bartjanvanrossum/actions/runs/38865052648"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-10-16T07:12:11.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "e8a8806b23aea5b25acac97c61ac5733df4fe301",
      "fileid": "https://r2.ropensci.org/00586a2a00e591e7928a12e3d97b9bb1d450a5c153116f26d904a4ee6b2e705c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bartjanvanrossum/actions/runs/38865052648"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.3",
      "date": "2026-10-16T07:27:18.000Z",
      "arch": "aarch64",
      "commit": "e8a8806b23aea5b25acac97c61ac5733df4fe301",
      "fileid": "https://r2.ropensci.org/38cf3176b30efd0a5bfa3d1847939d3c37a78d74e2470417505a67520d1bfe03",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bartjanvanrossum/actions/runs/38865052648"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.3",
      "date": "2026-10-16T07:20:12.000Z",
      "arch": "x86_64",
      "commit": "e8a8806b23aea5b25acac97c61ac5733df4fe301",
      "fileid": "https://r2.ropensci.org/4809bcb42d2c80fbea3b8e4ef39cfa1e4b3428625c0330eb8ceda7191a5f1a71",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bartjanvanrossum/actions/runs/38865052648"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0.3",
      "date": "2026-10-16T07:23:37.000Z",
      "arch": "aarch64",
      "commit": "e8a8806b23aea5b25acac97c61ac5733df4fe301",
      "fileid": "https://r2.ropensci.org/f06bbbd4804649e2bbd60cd47ce7e9ac525ed25a5f3043dc5e751f54b6fd5753",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bartjanvanrossum/actions/runs/38865052648"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0.3",
      "date": "2026-10-16T07:20:26.000Z",
      "arch": "x86_64",
      "commit": "e8a8806b23aea5b25acac97c61ac5733df4fe301",
      "fileid": "https://r2.ropensci.org/6b30f27039b3dc5e04ecc4a0e38b921b9196bdff6ecd38978d8fcd0555c2be7f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bartjanvanrossum/actions/runs/38865052648"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.3",
      "date": "2026-10-16T07:12:09.000Z",
      "arch": "emscripten",
      "commit": "e8a8806b23aea5b25acac97c61ac5733df4fe301",
      "fileid": "https://r2.ropensci.org/4829d22b2250888279cb7c4717e4ad079b1298c48ae7cc55138dd0a1c0180ccd",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bartjanvanrossum/actions/runs/38865052648"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-10-16T07:15:32.000Z",
      "arch": "aarch64",
      "commit": "e8a8806b23aea5b25acac97c61ac5733df4fe301",
      "fileid": "https://r2.ropensci.org/3dcb71a46e04867470f25615c4c8681472118effa6a387935a2839646e7f5187",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bartjanvanrossum/actions/runs/38865052648"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-10-16T07:11:15.000Z",
      "arch": "x86_64",
      "commit": "e8a8806b23aea5b25acac97c61ac5733df4fe301",
      "fileid": "https://r2.ropensci.org/bb9bfcfd64fec289ae14c6a7a8a9dd486a798ed6f293c622655b00c6f94d0f17",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bartjanvanrossum/actions/runs/38865052648"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-10-16T07:11:20.000Z",
      "arch": "x86_64",
      "commit": "e8a8806b23aea5b25acac97c61ac5733df4fe301",
      "fileid": "https://r2.ropensci.org/8aad0c2a96a6e7c5b88431514a675bc818752acbcbfc039987ffa71e02ad5a4f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bartjanvanrossum/actions/runs/38865052648"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-10-16T07:15:22.000Z",
      "arch": "aarch64",
      "commit": "e8a8806b23aea5b25acac97c61ac5733df4fe301",
      "fileid": "https://r2.ropensci.org/73b3ab66057fe9fe69cab6527ec209cd7ade2e5d8234fa6d9766a12ed5399152",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bartjanvanrossum/actions/runs/38865052648"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-10-16T07:11:07.000Z",
      "arch": "x86_64",
      "commit": "e8a8806b23aea5b25acac97c61ac5733df4fe301",
      "fileid": "https://r2.ropensci.org/7426cfd1041fd6be5de4cc83c68c869a40e6fae06f513b53fae91107e07513f7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bartjanvanrossum/actions/runs/38865052648"
    }
  ]
}