{
  "_id": "6a5c7cf09baadeef8ab509eb",
  "Package": "qtlhot",
  "Version": "1.2.10",
  "Date": "2026-01-19",
  "Authors@R": "c(person(given = c(\"Elias\", \"Chaibub\"),\nfamily = \"Neto\",\nrole = \"aut\",\nemail = \"echaibub@hotmail.com\"),\nperson(given = c(\"Brian\", \"S\"),\nfamily = \"Yandell\",\nrole = \"aut\",\nemail = \"brian.yandell@wisc.edu\"),\nperson(given = c(\"Brian\", \"S.\"),\nfamily = \"Yandell\",\nrole = \"cre\",\nemail = \"brian.yandell@wisc.edu\"))",
  "Title": "Inference for QTL Hotspots",
  "Description": "Functions to infer co-mapping trait hotspots and causal\nmodels. Chaibub Neto E, Keller MP, Broman AF, Attie AD, Jansen\nRC, Broman KW, Yandell BS (2012) Quantile-based permutation\nthresholds for QTL hotspots. Genetics 191 : 1355-1365.\n<doi:10.1534/genetics.112.139451>. Chaibub Neto E, Broman AT,\nKeller MP, Attie AD, Zhang B, Zhu J, Yandell BS (2013) Modeling\ncausality for pairs of phenotypes in system genetics. Genetics\n193 : 1003-1013. <doi:10.1534/genetics.112.147124>.",
  "Maintainer": "Brian S. Yandell <brian.yandell@wisc.edu>",
  "LazyLoad": "true",
  "LazyData": "true",
  "License": "GPL (>= 2)",
  "URL": "https://github.com/byandell-sysgen/qtlhot",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "Repository": "https://byandell-sysgen.r-universe.dev",
  "Date/Publication": "2026-01-19 15:51:09 UTC",
  "RemoteUrl": "https://github.com/byandell-sysgen/qtlhot",
  "RemoteRef": "HEAD",
  "RemoteSha": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-19 07:26:58 UTC",
    "User": "root"
  },
  "Author": "Elias Chaibub Neto [aut],\nBrian S Yandell [aut],\nBrian S. Yandell [cre]",
  "_user": "byandell-sysgen",
  "_type": "src",
  "_file": "qtlhot_1.2.10.tar.gz",
  "_fileid": "https://r2.ropensci.org/0f8c888d09a6754797d5f433d7344a1b01814b29fe06f1bce57817687158b34f",
  "_filesize": 1667126,
  "_sha256": "0f8c888d09a6754797d5f433d7344a1b01814b29fe06f1bce57817687158b34f",
  "_expires": "2026-10-27T07:29:51.000Z",
  "_created": "2026-07-19T07:26:58.000Z",
  "_published": "2026-07-19T07:29:52.893Z",
  "_jobs": [
    {
      "job": 88169251856,
      "time": 138,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8439653294"
    },
    {
      "job": 88169251866,
      "time": 124,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8439651143"
    },
    {
      "job": 88169251891,
      "time": 100,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8439647497"
    },
    {
      "job": 88169251862,
      "time": 78,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8439644096"
    },
    {
      "job": 88169011003,
      "time": 190,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8439631762"
    },
    {
      "job": 88169251868,
      "time": 104,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8439647799"
    },
    {
      "job": 88169251865,
      "time": 85,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8439645194"
    },
    {
      "job": 88169251858,
      "time": 77,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8439643834"
    },
    {
      "job": 88169251893,
      "time": 64,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8439642130"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/byandell-sysgen/actions/runs/29678033574",
  "_status": "success",
  "_upstream": "https://github.com/byandell-sysgen/qtlhot",
  "_commit": {
    "id": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6",
    "author": "byandell <byandell@wisc.edu>",
    "committer": "byandell <byandell@wisc.edu>",
    "message": "Prep for CRAN: fix .Rbuildignore, update R dependency, bump version to 1.2.10\n",
    "time": 1768837869
  },
  "_maintainer": {
    "name": "Brian S. Yandell",
    "email": "brian.yandell@wisc.edu"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "stats",
      "role": "Depends"
    },
    {
      "package": "qtl",
      "role": "Depends"
    },
    {
      "package": "mnormt",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Depends"
    },
    {
      "package": "corpcor",
      "role": "Depends"
    },
    {
      "package": "broman",
      "role": "Depends"
    },
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "byandell-sysgen",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-50",
      "n": 18
    },
    {
      "week": "2025-52",
      "n": 2
    },
    {
      "week": "2026-04",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 3,
  "_contributors": [
    {
      "user": "byandell",
      "count": 70,
      "uuid": 325732
    }
  ],
  "_userbio": {
    "uuid": 184665331,
    "type": "organization",
    "name": "byandell-sysgen",
    "followers": 0
  },
  "_downloads": {
    "count": 226,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/qtlhot"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/byandell-sysgen/qtlhot",
  "_searchresults": 42,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/qtlhot.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/byandell-sysgen/qtlhot",
  "_realowner": "byandell-sysgen",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.5.2",
      "date": "2012-05-31"
    },
    {
      "version": "0.6.1",
      "date": "2012-09-17"
    },
    {
      "version": "0.6.4",
      "date": "2012-09-27"
    },
    {
      "version": "0.6.6",
      "date": "2012-10-02"
    },
    {
      "version": "0.6.7",
      "date": "2012-10-23"
    },
    {
      "version": "0.7.0",
      "date": "2012-10-25"
    },
    {
      "version": "0.7.2",
      "date": "2012-11-06"
    },
    {
      "version": "0.8.3",
      "date": "2012-12-03"
    },
    {
      "version": "0.8.6",
      "date": "2013-05-07"
    },
    {
      "version": "0.9.0",
      "date": "2013-09-19"
    },
    {
      "version": "1.0.4",
      "date": "2018-04-05"
    },
    {
      "version": "1.2.10",
      "date": "2026-01-19"
    }
  ],
  "_exports": [
    "CitTests",
    "CMSTtests",
    "CMSTtestsList",
    "CombineTests",
    "FitAllTests",
    "GetCandReg",
    "GetCisCandReg",
    "GetCoMappingTraits",
    "GetCommonQtls",
    "highlod",
    "hotperm",
    "hotsize",
    "include.hotspots",
    "JoinTestOutputs",
    "neqtl",
    "PrecTpFpMatrix",
    "pull.highlod",
    "quantile_highlod",
    "quantile_hotperm",
    "sim.null.cross",
    "SimCrossCausal"
  ],
  "_datasets": [
    {
      "name": "CMSTCross",
      "title": "MST Sample Cross object",
      "object": "CMSTCross",
      "class": [
        "bc",
        "cross"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hotperm1",
      "title": "Hotspot Permutation Sample",
      "object": "hotperm1",
      "class": [
        "hotperm",
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "add.phenos",
      "title": "Add phenotypes to cross object.",
      "topics": [
        "add.phenos"
      ]
    },
    {
      "page": "CMSTCross",
      "title": "MST Sample Cross object",
      "topics": [
        "CMSTCross"
      ]
    },
    {
      "page": "CMSTtests",
      "title": "Perform CMST Tests on cross object",
      "topics": [
        "CMSTtests",
        "CMSTtestsList",
        "GetCisCandReg"
      ]
    },
    {
      "page": "filter.threshold",
      "title": "Summary of threshold results",
      "topics": [
        "filter.threshold"
      ]
    },
    {
      "page": "FitAllTests",
      "title": "Determine false positive and true positive rates for known targets.",
      "topics": [
        "CitTests",
        "CombineTests",
        "FitAllTests",
        "JoinTestOutputs"
      ]
    },
    {
      "page": "GetCandReg",
      "title": "Get genetic information on candidate regulators and co-mapping traits.",
      "topics": [
        "GetCandReg",
        "GetCoMappingTraits"
      ]
    },
    {
      "page": "GetCommonQtls",
      "title": "Get common QTLs for phenotypes",
      "topics": [
        "GetCommonQtls"
      ]
    },
    {
      "page": "highlod",
      "title": "Pull high LOD values with chr and pos.",
      "topics": [
        "highlod",
        "max.highlod",
        "plot.highlod",
        "print.highlod",
        "pull.highlod",
        "summary.highlod"
      ]
    },
    {
      "page": "hotperm",
      "title": "Conduct NL and N permutation tests",
      "topics": [
        "hotperm",
        "plot.hotperm",
        "print.hotperm",
        "print.summary.hotperm",
        "summary.hotperm"
      ]
    },
    {
      "page": "hotperm1",
      "title": "Hotspot Permutation Sample",
      "topics": [
        "hotperm1"
      ]
    },
    {
      "page": "hotsize",
      "title": "Hotspot size routines.",
      "topics": [
        "hotsize",
        "hotsize.highlod",
        "hotsize.scanone",
        "max.hotsize",
        "plot.hotsize",
        "print.hotsize",
        "summary.hotsize"
      ]
    },
    {
      "page": "include.hotspots",
      "title": "Generate hotspots for the simulated examples in the manuscript.",
      "topics": [
        "include.hotspots"
      ]
    },
    {
      "page": "neqtl",
      "title": "neqtl.R Ported from http://github.com/kbroman/neqtl",
      "topics": [
        "neqtl"
      ]
    },
    {
      "page": "parallel.qtlhot",
      "title": "Code for parallelizing R/qtlhot.",
      "topics": [
        "parallel.qtlhot"
      ]
    },
    {
      "page": "PrecTpFpMatrix",
      "title": "Compute Precision, True Positives, and False Positives",
      "topics": [
        "PrecTpFpMatrix"
      ]
    },
    {
      "page": "quantile_highlod",
      "title": "Compute Quantiles of High LOD Scores",
      "topics": [
        "quantile_highlod"
      ]
    },
    {
      "page": "quantile_hotperm",
      "title": "Compute Quantiles for Hotperm Results",
      "topics": [
        "quantile_hotperm"
      ]
    },
    {
      "page": "sim.hotspot",
      "title": "Wrapper routine for simulations.",
      "topics": [
        "sim.hotspot"
      ]
    },
    {
      "page": "sim.null.cross",
      "title": "Generates a \"null dataset\" cross",
      "topics": [
        "sim.null.cross"
      ]
    },
    {
      "page": "SimCrossCausal",
      "title": "Simulate Cross for Causal Tests",
      "topics": [
        "SimCrossCausal"
      ]
    },
    {
      "page": "ww.perm",
      "title": "Conduct West-Wu (Q) permutation tests",
      "topics": [
        "print.ww.perm",
        "summary.ww.perm",
        "ww.perm"
      ]
    }
  ],
  "_readme": "https://github.com/byandell-sysgen/qtlhot/raw/HEAD/README.md",
  "_rundeps": [
    "broman",
    "cli",
    "corpcor",
    "cpp11",
    "farver",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "mnormt",
    "qtl",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "cmst.Rmd",
      "filename": "cmst.pdf",
      "title": "Causal Model Selection Hypothesis Tests in Systems Genetics: \\ a tutorial",
      "author": "Elias Chaibub Neto and Brian S. Yandell",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Motivation",
        "Overview",
        "Basic functionality",
        "Other Functions",
        "References"
      ],
      "created": "2025-12-08 19:29:36",
      "modified": "2025-12-09 01:51:14",
      "commits": 3
    },
    {
      "source": "qtlhot.Rmd",
      "filename": "qtlhot.pdf",
      "title": "Qtlhot Tutorial",
      "author": "Elias Chaibub Neto and Brian S. Yandell",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Motivation",
        "Overview",
        "Basic functionality with No Real Hotspots",
        "Example with Uncorrelated Phenotypes",
        "References"
      ],
      "created": "2025-12-08 19:29:36",
      "modified": "2025-12-09 20:46:37",
      "commits": 4
    }
  ],
  "_score": 5.577491799837226,
  "_indexed": true,
  "_nocasepkg": "qtlhot",
  "_universes": [
    "byandell-sysgen"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.10",
      "date": "2026-07-19T07:29:11.000Z",
      "distro": "resolute",
      "commit": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6",
      "fileid": "https://r2.ropensci.org/40c40a8a6442c6209172c205f2f613d7eccd67cb249a4f70fff9d9f79b420198",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/byandell-sysgen/actions/runs/29678033574"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.2.10",
      "date": "2026-07-19T07:28:59.000Z",
      "distro": "resolute",
      "commit": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6",
      "fileid": "https://r2.ropensci.org/0a452a31e55a4fc988d5ec714bb1c61efa7f5badbd7ac78e7580ce883cdfadcc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/byandell-sysgen/actions/runs/29678033574"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2.10",
      "date": "2026-07-19T07:28:39.000Z",
      "commit": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6",
      "fileid": "https://r2.ropensci.org/665610c9402696ed4f27ff2c129d8b57fdc263edd85dc6fd8fde51631163ba30",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/byandell-sysgen/actions/runs/29678033574"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.2.10",
      "date": "2026-07-19T07:28:19.000Z",
      "commit": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6",
      "fileid": "https://r2.ropensci.org/6ac352149a6674917a4606bdbcbc6513d2ce4eb61ec5586965aedc3d3602c051",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/byandell-sysgen/actions/runs/29678033574"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.2.10",
      "date": "2026-07-19T07:28:57.000Z",
      "commit": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6",
      "fileid": "https://r2.ropensci.org/4f78511e852543cd014c9f101a9002e33c1d04e6ab4cb0d3a939ad6e50bfbf28",
      "status": "success",
      "buildurl": "https://github.com/r-universe/byandell-sysgen/actions/runs/29678033574"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.2.10",
      "date": "2026-07-19T07:28:10.000Z",
      "commit": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6",
      "fileid": "https://r2.ropensci.org/36848a2c8a64ff300397678891060603022d145ad78b16a9ab77e09a0df1bd60",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/byandell-sysgen/actions/runs/29678033574"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.2.10",
      "date": "2026-07-19T07:28:03.000Z",
      "commit": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6",
      "fileid": "https://r2.ropensci.org/d7d44ff606d352d423bcdb816c093f482b7886f78ed632870af5be5995ee890a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/byandell-sysgen/actions/runs/29678033574"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.2.10",
      "date": "2026-07-19T07:28:00.000Z",
      "commit": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6",
      "fileid": "https://r2.ropensci.org/8319a13c44e625e70e94d06cf2679d94a497377db269eac879cfbc5c0b73c551",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/byandell-sysgen/actions/runs/29678033574"
    }
  ]
}