{ "_id": "6a1ede6cb401979e7341035b", "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. 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. .", "Maintainer": "Brian S. Yandell ", "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": "2026-05-20 07:54:35 UTC", "User": "root" }, "Author": "Elias Chaibub Neto [aut],\nBrian S Yandell [aut],\nBrian S. Yandell [cre]", "MD5sum": "86fedf360a72ec1206b6faf4bec3f6f8", "_user": "byandell-sysgen", "_type": "src", "_file": "qtlhot_1.2.10.tar.gz", "_fileid": "da5aee0e936125470d4094f1fc344145e75def75ccdf05769d0243b542ace50f", "_filesize": 1666509, "_sha256": "da5aee0e936125470d4094f1fc344145e75def75ccdf05769d0243b542ace50f", "_created": "2026-05-20T07:54:35.000Z", "_published": "2026-06-02T13:45:16.075Z", "_distro": "noble", "_jobs": [ { "job": 79085263338, "time": 162, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7104340591" }, { "job": 79085264462, "time": 130, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7104329949" }, { "job": 79085263283, "time": 105, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7104321626" }, { "job": 79085263218, "time": 111, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7104322938" }, { "job": 79085263008, "time": 178, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7104287365" }, { "job": 79085262409, "time": 113, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7359468468" }, { "job": 79085263329, "time": 73, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7104311401" }, { "job": 79085264697, "time": 80, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7104313525" }, { "job": 79085264326, "time": 75, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7104312353" } ], "_buildurl": "https://github.com/r-universe/byandell-sysgen/actions/runs/26149105852", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/byandell-sysgen/qtlhot", "_commit": { "id": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6", "author": "byandell ", "committer": "byandell ", "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" }, "_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" }, "_downloads": { "count": 167, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/qtlhot" }, "_mentions": 1, "_devurl": "https://github.com/byandell-sysgen/qtlhot", "_searchresults": 33, "_rbuild": "4.6.0", "_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": 5.472756449317212, "_indexed": true, "_nocasepkg": "qtlhot", "_universes": [ "byandell-sysgen" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.2.10", "date": "2026-05-20T07:57:13.000Z", "distro": "noble", "commit": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6", "fileid": "c5d64344bee8bde0fc7d901b0fc3f5b5e60a71b2cca1ce6bbe8a51d6ae6e3786", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/byandell-sysgen/actions/runs/26149105852" }, { "r": "4.6.0", "os": "linux", "version": "1.2.10", "date": "2026-05-20T07:56:40.000Z", "distro": "noble", "commit": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6", "fileid": "157b9d35de1f5a22d279ae3b038ba607b93b2cd790841f71c4f2c1a99b8629d4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/byandell-sysgen/actions/runs/26149105852" }, { "r": "4.5.3", "os": "mac", "version": "1.2.10", "date": "2026-05-20T07:56:19.000Z", "commit": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6", "fileid": "df58b86ec298ea631529429b948582385ffbfe1a955b5dcafdeb35170adf2624", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/byandell-sysgen/actions/runs/26149105852" }, { "r": "4.6.0", "os": "mac", "version": "1.2.10", "date": "2026-05-20T07:56:25.000Z", "commit": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6", "fileid": "2049247c8fc79b2cfc5ac012000feb6c2dc9bda82b300e5367347088821dcd38", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/byandell-sysgen/actions/runs/26149105852" }, { "r": "4.7.0", "os": "win", "version": "1.2.10", "date": "2026-05-20T07:55:39.000Z", "commit": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6", "fileid": "ccfc0b4d80a6236558ff7b1aa1542f27e325c6b451ebb6a5de7e45166d339bf3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/byandell-sysgen/actions/runs/26149105852" }, { "r": "4.5.3", "os": "win", "version": "1.2.10", "date": "2026-05-20T07:55:45.000Z", "commit": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6", "fileid": "14ee0d46864b21971b00a27e665ac5187c35740e8315e47192a9a836c7be1bb6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/byandell-sysgen/actions/runs/26149105852" }, { "r": "4.6.0", "os": "win", "version": "1.2.10", "date": "2026-05-20T07:55:43.000Z", "commit": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6", "fileid": "7181895c7c7f907c1c24bf171e71347c143ba5f2d5c44059f570291834025b48", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/byandell-sysgen/actions/runs/26149105852" }, { "r": "4.6.0", "os": "wasm", "version": "1.2.10", "date": "2026-06-02T13:44:59.000Z", "commit": "eb8fe508bd8c4faa547e007e806e2dedfd6686f6", "fileid": "b76a8d8a5a113da40ecda568cc06eaabd61ea60326a564eed932f3aca551e4d5", "status": "success", "buildurl": "https://github.com/r-universe/byandell-sysgen/actions/runs/26149105852" } ] }