{ "_id": "6a227c7ccd65a98ecbd4edb3", "Package": "RepeatABEL", "Title": "GWAS for Multiple Observations on Related Individuals", "Version": "2.0", "Authors@R": "person(\"Lars\", \"Ronnegard\", , \"lars.ronnegard@slu.se\", role = c(\"aut\", \"cre\"))", "Description": "Performs genome-wide association studies (GWAS) on\nindividuals that are both related and have repeated\nmeasurements. For each Single Nucleotide Polymorphism (SNP), it\ncomputes score statistic based p-values for a linear mixed\nmodel including random polygenic effects and a random effect\nfor repeated measurements. The computed p-values can be\nvisualized in a Manhattan plot. For more details see Ronnegard\net al. (2016) and for more\nexamples see\n.", "License": "GPL", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "Collate": "'Compute_GRM2.R' 'Create_gwaa_data2.R' 'Create_gwaa_scan2.R'\n'SmoothSNPmatrix.R' 'chromosome.R' 'constructV.R'\n'estlambda2.R' 'snp.data.R' 'gwaa.data2.R' 'idnames.R'\n'keep_gwaa_data.R' 'map.R' 'nids.R' 'plot.scan.gwaa2.R'\n'preFitModel.R' 'rGLS.R' 'scan.gwaa2.R' 'simulate_PhenData.R'\n'simulate_gendata.R' 'snpnames.R' 'summary_scan_gwaa2.R'", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-05 07:33:52 UTC", "User": "root" }, "Author": "Lars Ronnegard [aut, cre]", "Maintainer": "Lars Ronnegard ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-01-06 11:00:15 UTC", "RemoteUrl": "https://github.com/cran/RepeatABEL", "RemoteRef": "HEAD", "RemoteSha": "7541db3ce11377ab3145e0b40eb9a4df8a2af971", "MD5sum": "3d9d9b900a9ae7bb2c4a4ad680fc8922", "_user": "cran", "_type": "src", "_file": "RepeatABEL_2.0.tar.gz", "_fileid": "86300d77ef826a1fd7ab960e6ae1bf12fb107c45836d5da8d97db7304be26dc0", "_filesize": 134267, "_sha256": "86300d77ef826a1fd7ab960e6ae1bf12fb107c45836d5da8d97db7304be26dc0", "_created": "2026-06-05T07:33:52.000Z", "_published": "2026-06-05T07:36:28.265Z", "_distro": "noble", "_jobs": [ { "job": 79684249547, "time": 118, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7431254156" }, { "job": 79684249562, "time": 121, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7431255217" }, { "job": 79683744747, "time": 215, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7431217205" }, { "job": 79684249579, "time": 94, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7431246636" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/27001765579", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/RepeatABEL", "_commit": { "id": "7541db3ce11377ab3145e0b40eb9a4df8a2af971", "author": "Lars Ronnegard ", "committer": "cran-robot ", "message": "version 2.0\n", "time": 1767697215 }, "_maintainer": { "name": "Lars Ronnegard", "email": "lars.ronnegard@slu.se" }, "_registered": true, "_dependencies": [ { "package": "hglm", "role": "Depends" }, { "package": "methods", "role": "Depends" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-02", "n": 1 } ], "_tags": [ { "name": "2.0", "date": "2026-01-06" } ], "_stars": 1, "_contributors": [ { "user": "larsronn", "count": 2, "uuid": 70625922 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 445, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RepeatABEL" }, "_searchresults": 18, "_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/RepeatABEL.html", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2015-11-24" }, { "version": "1.1", "date": "2016-08-19" }, { "version": "2.0", "date": "2026-01-06" } ], "_exports": [ "chromosome", "compute.GRM", "constructV", "Create_gwaa_data2", "Create_gwaa_scan2", "estlambda", "idnames", "nids", "preFitModel", "rGLS", "simulate_gendata", "simulate_PhenData" ], "_help": [ { "page": "chromosome", "title": "Extracts the chromosome numbers", "topics": [ "chromosome" ] }, { "page": "compute.GRM", "title": "Computes a Genetic Relationship Matrix from a GenABEL-like object", "topics": [ "compute.GRM" ] }, { "page": "constructV", "title": "Constructs the (co)variance matrix for y", "topics": [ "constructV" ] }, { "page": "Create_gwaa_data2", "title": "Creates a gwaa.data2 object", "topics": [ "Create_gwaa_data2" ] }, { "page": "Create_gwaa_scan2", "title": "Creates a scan.gwaa2 object", "topics": [ "Create_gwaa_scan2" ] }, { "page": "estlambda", "title": "Function to estimate lambda", "topics": [ "estlambda" ] }, { "page": "gwaa.data2-class", "title": "An S4 class to represent GWAS input data", "topics": [ "gwaa.data2-class" ] }, { "page": "idnames", "title": "Extracts the id names", "topics": [ "idnames" ] }, { "page": "keep_gwaa_data", "title": "A function to subset an gwaa.data2 object", "topics": [ "keep_gwaa_data" ] }, { "page": "map", "title": "Extracts the map information", "topics": [ "map" ] }, { "page": "nids", "title": "Extracts the number of ids", "topics": [ "nids" ] }, { "page": "plot.scan.gwaa2", "title": "Function to plot P-values as a Manhattan plot", "topics": [ "plot.scan.gwaa2" ] }, { "page": "preFitModel", "title": "Fits a linear mixed model (without fixed SNP effects) and computes the fitted variance-covariance matrix for later use in the rGLS function.", "topics": [ "preFitModel" ] }, { "page": "rGLS", "title": "GWAS for Studies having Repeated Measurements on Related Individuals", "topics": [ "rGLS" ] }, { "page": "scan.gwaa2-class", "title": "An S4 class to represent SNP data", "topics": [ "scan.gwaa2-class" ] }, { "page": "simulate_gendata", "title": "Function to simulate genotype data for the RepeatABEL package.", "topics": [ "simulate_gendata" ] }, { "page": "simulate_PhenData", "title": "Simulation function for the RepeatABEL package.", "topics": [ "simulate_PhenData" ] }, { "page": "SmoothSNPmatrix", "title": "Imputes column means to missing genotypes", "topics": [ "SmoothSNPmatrix" ] }, { "page": "snp.data", "title": "An S4 class to represent SNP data", "topics": [ "snp.data" ] }, { "page": "snpnames", "title": "Extracts the snpnames", "topics": [ "snpnames" ] }, { "page": "summary.scan.gwaa2", "title": "Summary function for the rGLS output", "topics": [ "summary.scan.gwaa2" ] } ], "_rundeps": [ "hglm", "hglm.data", "lattice", "MASS", "Matrix", "sp" ], "_score": 1.255272505103306, "_indexed": true, "_nocasepkg": "repeatabel", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.0", "date": "2026-06-05T07:35:42.000Z", "distro": "noble", "commit": "7541db3ce11377ab3145e0b40eb9a4df8a2af971", "fileid": "9d81939c395a791e4b5db7bdd662f424ddb609135972604574feff46335cdf06", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/27001765579" }, { "r": "4.6.0", "os": "linux", "version": "2.0", "date": "2026-06-05T07:35:46.000Z", "distro": "noble", "commit": "7541db3ce11377ab3145e0b40eb9a4df8a2af971", "fileid": "14c7c70f5238a207e8ff97c614c4cfc2dc6c047f850f2e6931811731f4d298e4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/27001765579" }, { "r": "4.6.0", "os": "wasm", "version": "2.0", "date": "2026-06-05T07:35:46.000Z", "commit": "7541db3ce11377ab3145e0b40eb9a4df8a2af971", "fileid": "6d74fc4d4a4748bb3da6446b946b859f4d19df5a7c01bb81e310d735cc796c56", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/27001765579" } ] }