{ "_id": "6a1ad8f81d7bb097a09e71d3", "Type": "Package", "Package": "qtl2pleio", "Title": "Testing Pleiotropy in Multiparental Populations", "Version": "1.4.4", "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 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) in that\nour test accommodates multiparental populations.", "License": "MIT + file LICENSE", "URL": "https://github.com/fboehm/qtl2pleio", "BugReports": "https://github.com/fboehm/qtl2pleio/issues", "Encoding": "UTF-8", "Language": "en-US", "NeedsCompilation": "yes", "RoxygenNote": "7.3.3", "Repository": "https://fboehm.r-universe.dev", "Date/Publication": "2026-05-29 13:12:10 UTC", "RemoteUrl": "https://github.com/fboehm/qtl2pleio", "RemoteRef": "HEAD", "RemoteSha": "d1dfcf7ab672e918c23f465524f42fb4e33e053a", "Packaged": { "Date": "2026-05-30 09:11:04 UTC", "User": "root" }, "Author": "Frederick J Boehm [aut, cre] (ORCID:\n)", "Maintainer": "Frederick J Boehm ", "MD5sum": "a817cdee62e71f448a6f63ca386e9c5b", "_user": "fboehm", "_type": "src", "_file": "qtl2pleio_1.4.4.tar.gz", "_fileid": "b2fa4c5fbe35fb25dcefa0918e6b6c4e3d244538ac0b866647e04252cea85aca", "_filesize": 318253, "_sha256": "b2fa4c5fbe35fb25dcefa0918e6b6c4e3d244538ac0b866647e04252cea85aca", "_created": "2026-05-30T09:11:04.000Z", "_published": "2026-05-30T12:32:56.167Z", "_distro": "noble", "_jobs": [ { "job": 78638831063, "time": 180, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7307101841" }, { "job": 78638831066, "time": 208, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307110710" }, { "job": 78638831060, "time": 173, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7307101271" }, { "job": 78638831057, "time": 194, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307109438" }, { "job": 78638831050, "time": 138, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7308191816" }, { "job": 78638831051, "time": 262, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7307110389" }, { "job": 78638831049, "time": 115, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7308185505" }, { "job": 78638831056, "time": 364, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307121770" }, { "job": 78638630702, "time": 231, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307084145" }, { "job": 78638831038, "time": 146, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307104829" }, { "job": 78638831043, "time": 188, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7307109375" }, { "job": 78638831040, "time": 161, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7307106784" }, { "job": 78638831053, "time": 169, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7307107496" } ], "_buildurl": "https://github.com/r-universe/fboehm/actions/runs/26650024021", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/fboehm/qtl2pleio", "_commit": { "id": "d1dfcf7ab672e918c23f465524f42fb4e33e053a", "author": "Frederick Boehm ", "committer": "Frederick Boehm ", "message": "fix: deleted extra parenthesis\n", "time": 1780060330 }, "_maintainer": { "name": "Frederick J Boehm", "email": "frederick.boehm@gmail.com", "login": "fboehm", "orcid": "0000-0002-1644-5931", "description": "I study biostatistics, with a focus in statistical genetics. I strive to understand how our genes influence our health and biology.", "uuid": 4155196 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.2", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppEigen", "role": "LinkingTo" }, { "package": "dplyr", "role": "Imports" }, { "package": "gemma2", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "covr", "role": "Suggests" }, { "package": "mvtnorm", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "broman", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" }, { "package": "qtl2", "role": "Suggests" }, { "package": "parallelly", "role": "Suggests" } ], "_owner": "fboehm", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-09", "n": 1 }, { "week": "2026-17", "n": 4 }, { "week": "2026-22", "n": 3 } ], "_tags": [], "_topics": [ "multiparental-populations", "quantitative-genetics", "quantitative-trait", "cpp" ], "_stars": 6, "_contributors": [ { "user": "fboehm", "count": 649, "uuid": 4155196 }, { "user": "kbroman", "count": 12, "uuid": 53972 }, { "user": "aquinon3", "count": 1, "uuid": 108319239 }, { "user": "kyleniemeyer", "count": 1, "uuid": 190432 } ], "_userbio": { "uuid": 4155196, "type": "user", "name": "Frederick Boehm", "description": "I study biostatistics, with a focus in statistical genetics. I strive to understand how our genes influence our health and biology." }, "_downloads": { "count": 507, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/qtl2pleio" }, "_mentions": 2, "_devurl": "https://github.com/fboehm/qtl2pleio", "_searchresults": 28, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/qtl2pleio.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/fboehm/qtl2pleio", "_realowner": "fboehm", "_cranurl": true, "_releases": [ { "version": "1.2.3", "date": "2019-11-05" }, { "version": "1.3.0", "date": "2020-06-30" }, { "version": "1.4.1", "date": "2020-10-29" }, { "version": "1.4.3", "date": "2020-12-03" }, { "version": "1.4.4", "date": "2026-04-26" } ], "_exports": [ "%>%", "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" ], "_help": [ { "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", "topics": [ "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", "topics": [ "subset_kinship" ] } ], "_readme": "https://github.com/fboehm/qtl2pleio/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "dplyr", "farver", "gemma2", "generics", "ggplot2", "glue", "gtable", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "pillar", "pkgconfig", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "rlang", "S7", "scales", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 5.1795517911651885, "_indexed": true, "_nocasepkg": "qtl2pleio", "_universes": [ "fboehm" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.4.4", "date": "2026-05-30T09:14:06.000Z", "distro": "noble", "arch": "aarch64", "commit": "d1dfcf7ab672e918c23f465524f42fb4e33e053a", "fileid": "aa9b8afd1ceeb9bbf0cddd550bd27c2ad20bb8ccf507e91d15050cfb92c2a2f5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fboehm/actions/runs/26650024021" }, { "r": "4.7.0", "os": "linux", "version": "1.4.4", "date": "2026-05-30T09:15:22.000Z", "distro": "noble", "arch": "x86_64", "commit": "d1dfcf7ab672e918c23f465524f42fb4e33e053a", "fileid": "a94713602f4f9dc9ac69d1e961b185836927c413927a17d5b9097e53f9879d33", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fboehm/actions/runs/26650024021" }, { "r": "4.6.0", "os": "linux", "version": "1.4.4", "date": "2026-05-30T09:13:59.000Z", "distro": "noble", "arch": "aarch64", "commit": "d1dfcf7ab672e918c23f465524f42fb4e33e053a", "fileid": "d8e1da244b8b12fb63978906c429742bde7dc067f9294ae172428c85edf79652", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fboehm/actions/runs/26650024021" }, { "r": "4.6.0", "os": "linux", "version": "1.4.4", "date": "2026-05-30T09:15:14.000Z", "distro": "noble", "arch": "x86_64", "commit": "d1dfcf7ab672e918c23f465524f42fb4e33e053a", "fileid": "21fe966bbed0361abe144e5864fcfcbf8f70b1fc64c7d6f08cc348d9def395e9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fboehm/actions/runs/26650024021" }, { "r": "4.5.3", "os": "mac", "version": "1.4.4", "date": "2026-05-30T12:31:45.000Z", "arch": "aarch64", "commit": "d1dfcf7ab672e918c23f465524f42fb4e33e053a", "fileid": "13033d34a39688f799bd85174edf189aa70e920cf1dcb444d25db56bd2749ec4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fboehm/actions/runs/26650024021" }, { "r": "4.5.3", "os": "mac", "version": "1.4.4", "date": "2026-05-30T09:14:49.000Z", "arch": "x86_64", "commit": "d1dfcf7ab672e918c23f465524f42fb4e33e053a", "fileid": "ac2dd2ab2ce8ec4d9a997bb9436d7e746bd1c212084e9a4da82d4c2ed60f02aa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fboehm/actions/runs/26650024021" }, { "r": "4.6.0", "os": "mac", "version": "1.4.4", "date": "2026-05-30T12:30:55.000Z", "arch": "aarch64", "commit": "d1dfcf7ab672e918c23f465524f42fb4e33e053a", "fileid": "b8e618b7d3c5ffcb24eb3e133466c4c432364e5b9f1d3be78321029cf28dbd05", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fboehm/actions/runs/26650024021" }, { "r": "4.6.0", "os": "mac", "version": "1.4.4", "date": "2026-05-30T09:15:52.000Z", "arch": "x86_64", "commit": "d1dfcf7ab672e918c23f465524f42fb4e33e053a", "fileid": "554ad161844f3a3b6a5fa85bf8074fa7382b5330de0c0932d80458e1288dfce6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fboehm/actions/runs/26650024021" }, { "r": "4.6.0", "os": "wasm", "version": "1.4.4", "date": "2026-05-30T09:15:10.000Z", "arch": "emscripten", "commit": "d1dfcf7ab672e918c23f465524f42fb4e33e053a", "fileid": "df5b18c02820d64c61de373c6fe7ba986b478089f44197fcd4a264259087bcb9", "status": "success", "buildurl": "https://github.com/r-universe/fboehm/actions/runs/26650024021" }, { "r": "4.7.0", "os": "win", "version": "1.4.4", "date": "2026-05-30T09:14:35.000Z", "arch": "x86_64", "commit": "d1dfcf7ab672e918c23f465524f42fb4e33e053a", "fileid": "731dea66f3dafa37bd91e03126247d008eb1b2869d24b97b1de34a153a504ca5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fboehm/actions/runs/26650024021" }, { "r": "4.5.3", "os": "win", "version": "1.4.4", "date": "2026-05-30T09:14:12.000Z", "arch": "x86_64", "commit": "d1dfcf7ab672e918c23f465524f42fb4e33e053a", "fileid": "eaeff2f0010d48820290494c1544d91ce9adf3e47c4a8cba6e7f34c12b4d96b1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fboehm/actions/runs/26650024021" }, { "r": "4.6.0", "os": "win", "version": "1.4.4", "date": "2026-05-30T09:14:13.000Z", "arch": "x86_64", "commit": "d1dfcf7ab672e918c23f465524f42fb4e33e053a", "fileid": "a6b864ef9ff22e97b9e4a9cd93b31d074930c2f348b71f422fa61fd5b758ddb8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fboehm/actions/runs/26650024021" } ] }