{ "_id": "6ac0a5b191601a2ad2996bb4", "Package": "BIGDAWG", "Type": "Package", "Title": "Case-Cotrol Analysis of Multi-Allelic Loci", "Version": "3.1.0", "Date": "2026-04-29", "Authors@R": "c(person(\"Derek\",\"Pappas\",role = \"aut\",email = \"djpappas75@gmail.com\"),\nperson(\"Livia\",\"Tran\",role = \"aut\",email = \"Livia.Tran@ucsf.edu\"),\nperson(\"Steve\",\"Mack\",role = c(\"aut\", \"cre\"),email = \"Steven.Mack@ucsf.edu\"),\nperson(\"Jill\",\"Hollenbach\",role = \"aut\",email = \"Jill.Hollenbach@ucsf.edu\"))", "Maintainer": "Steve Mack ", "URL": "https://github.com/IgDAWG/BIGDAWG", "BugReports": "https://github.com/IgDAWG/BIGDAWG/issues", "Description": "Data sets and functions for chi-squared Hardy-Weinberg and\ncase-control association tests of highly polymorphic genetic\ndata [e.g., human leukocyte antigen (HLA) data]. Performs\nassociation tests at multiple levels of polymorphism\n(haplotype, locus and HLA amino-acids) as described in Pappas\nDJ, Marin W, Hollenbach JA, Mack SJ (2016)\n. Combines rare variants to a\ncommon class to account for sparse cells in tables as described\nby Hollenbach JA, Mack SJ, Thomson G, Gourraud PA (2012)\n.", "License": "GPL (>= 3)", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "Config/pak/sysreqs": "libxml2-dev", "Repository": "https://igdawg.r-universe.dev", "Date/Publication": "2026-04-30 05:25:10 UTC", "RemoteUrl": "https://github.com/igdawg/bigdawg", "RemoteRef": "HEAD", "RemoteSha": "7f006b2a27d0c2c4b2ffbc280585f713db5f6f66", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-01 07:49:43 UTC", "User": "root" }, "Author": "Derek Pappas [aut],\nLivia Tran [aut],\nSteve Mack [aut, cre],\nJill Hollenbach [aut]", "_user": "igdawg", "_type": "src", "_file": "BIGDAWG_3.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/a0891214e204a6ad91c4557cb0da4ecf892450268544b70d1a8515bb1c55f046", "_filesize": 1206018, "_sha256": "a0891214e204a6ad91c4557cb0da4ecf892450268544b70d1a8515bb1c55f046", "_expires": "2027-01-09T07:54:24.000Z", "_created": "2026-10-01T07:49:43.000Z", "_published": "2026-10-03T06:50:25.141Z", "_jobs": [ { "job": 111149535365, "time": 169, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11147842624" }, { "job": 111149535467, "time": 167, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11148510744" }, { "job": 111149534477, "time": 114, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 111149534366, "time": 89, "config": "macos-release-arm64", "r": "4.6.1", "check": "FAIL", "artifact": "" }, { "job": 111149534721, "time": 213, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11147581582" }, { "job": 111149535050, "time": 135, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11148335875" }, { "job": 111149535191, "time": 88, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11147562833" }, { "job": 111149534435, "time": 63, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 111149534469, "time": 49, "config": "windows-release-x86_64", "r": "4.6.1", "check": "FAIL", "artifact": "" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/igdawg/actions/runs/36832252777", "_status": "success", "_upstream": "https://github.com/igdawg/bigdawg", "_commit": { "id": "7f006b2a27d0c2c4b2ffbc280585f713db5f6f66", "author": "sjmack ", "committer": "sjmack ", "message": "Version 3.1.0 29APR2026\nAddressed issue in L.R() for allele binning.\nAdded the Data.Type parameter to the BIGDAWG() function.\nUpdated and corrected URLs.\nUpdated DESCRIPTION.\n", "time": 1777526710 }, "_maintainer": { "name": "Steve Mack", "email": "steven.mack@ucsf.edu", "login": "sjmack", "description": "", "uuid": 8935284 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "XML", "role": "Imports" }, { "package": "haplo.stats", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "igdawg", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2026-18", "n": 1 } ], "_tags": [], "_stars": 4, "_contributors": [ { "user": "pappasd", "count": 95, "uuid": 10930633 }, { "user": "sjmack", "count": 1, "uuid": 8935284 } ], "_userbio": { "uuid": 25827834, "type": "user", "name": "Immunogenomics Data Analysis Working Group", "followers": 4, "description": "IgDAWG is a collaboration of histocompatibility and immunogenetics investigators who share the goal of facilitating the sharing of immunogenomic data." }, "_downloads": { "count": 596, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BIGDAWG" }, "_mentions": 7, "_devurl": "https://github.com/igdawg/bigdawg", "_searchresults": 4, "_rbuild": "4.6.1", "_assets": [ "extra/BIGDAWG.html", "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" ], "_homeurl": "https://github.com/igdawg/bigdawg", "_realowner": "igdawg", "_cranurl": true, "_releases": [ { "version": "1.1", "date": "2015-06-13" }, { "version": "1.1.1", "date": "2015-10-29" }, { "version": "1.2.1", "date": "2015-11-10" }, { "version": "1.2.6", "date": "2016-02-19" }, { "version": "1.2.8", "date": "2016-02-29" }, { "version": "1.3.4", "date": "2016-04-09" }, { "version": "1.4.0", "date": "2016-05-14" }, { "version": "1.5.4", "date": "2016-08-28" }, { "version": "1.5.5", "date": "2016-08-30" }, { "version": "1.13", "date": "2017-07-08" }, { "version": "1.14", "date": "2017-07-10" }, { "version": "1.14.2", "date": "2017-07-19" }, { "version": "1.16", "date": "2017-09-06" }, { "version": "2.1", "date": "2018-02-08" }, { "version": "2.3", "date": "2019-11-12" }, { "version": "2.3.1", "date": "2020-10-08" }, { "version": "2.3.6", "date": "2021-02-11" }, { "version": "3.0.3", "date": "2021-11-17" }, { "version": "3.1.0", "date": "2026-04-30" } ], "_exports": [ "A", "A.wrapper", "AA.df.check", "AA.df.cs", "AAtable.builder", "AlignmentFilter", "AlignObj.Create", "AlignObj.Update", "Append.System", "BIGDAWG", "Build.Matrix", "buildHAPnames", "buildHAPsets", "cci", "cci.pval", "cci.pval.list", "Check.Cores", "Check.Data", "Check.Params", "Check.Params.GLS", "CheckAlleles", "CheckHLA", "CheckLoci", "CheckRelease", "CheckString.Allele", "CheckString.Locus", "Condense.EPL", "Create.Null.Table", "DRB345.Check.Wrapper", "DRB345.Check.Zygosity", "DRB345.Exp", "DRB345.parser", "Err.Log", "EVSremoval", "Exon.Filter", "ExonPtnAlign.Create", "ExonPtnList", "Filler", "Format.Allele", "Format.Tab", "getAllele.Count", "getCS.Mat", "getCS.stat", "GetField", "getFileName", "GetFiles", "getHap", "getObsFreq", "GL2Tab.Loci", "GL2Tab.Sub", "GL2Tab.wrapper", "GLSconvert", "H.MC", "H.MC.wrapper", "HLA_data", "HWE", "HWE.ChiSq", "HWE.wrapper", "L", "L.wrapper", "make2x2", "makeComb", "MergeData_Output", "PgrpExtract", "PgrpFormat", "PreCheck", "prepData", "rmABstrings", "RunChiSq", "RunChiSq_c", "Stripper", "summaryGeno.2", "Tab2GL.Loci", "Tab2GL.Sub", "Tab2GL.wrapper", "TableMaker", "UpdateRelease" ], "_help": [], "_readme": "https://github.com/igdawg/bigdawg/raw/HEAD/README.md", "_rundeps": [ "arsenal", "evaluate", "glue", "haplo.stats", "highr", "knitr", "MASS", "xfun", "XML", "yaml" ], "_vignettes": [ { "source": "BIGDAWG.Rmd", "filename": "BIGDAWG.html", "title": "BIGDAWG", "author": "Derek Pappas, Ph.D. (djpappas75@gmail.com)", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Input Data", "Data Output", "Error Messages and Codes", "Known Issues", "Parameters", "Examples", "Updating the bundled IMGT/HLA protein alignment", "Updating BIGDAWG to latest developmental versions" ], "created": "2021-01-27 06:41:58", "modified": "2026-04-30 05:25:10", "commits": 21 }, { "source": "GLSconvert.Rmd", "filename": "GLSconvert.html", "title": "GLSconvert", "author": "Derek Pappas, Ph.D. (dpappas@chori.org)", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Anatomy of a GL String", "Input Data", "Data Output", "Parameters", "Examples" ], "created": "2021-01-27 06:41:58", "modified": "2022-10-18 17:58:32", "commits": 3 } ], "_score": 5.924279286061882, "_indexed": true, "_nocasepkg": "bigdawg", "_universes": [ "igdawg", "sjmack" ], "_binaries": [ { "r": "4.5.3", "os": "mac", "version": "3.1.0", "date": "2026-09-01T06:51:35.000Z", "commit": "7f006b2a27d0c2c4b2ffbc280585f713db5f6f66", "fileid": "https://r2.ropensci.org/38ed8a31cce99ed920494856b512dcf9c1c7af542795fea3bb070db268f94b18", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/igdawg/actions/runs/33478427788" }, { "r": "4.6.1", "os": "mac", "version": "3.1.0", "date": "2026-09-01T06:53:32.000Z", "commit": "7f006b2a27d0c2c4b2ffbc280585f713db5f6f66", "fileid": "https://r2.ropensci.org/8b6a6b29e34952df78d5ea8c5175986caabd63220fbdcc5e78a1441fd99ab929", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/igdawg/actions/runs/33478427788" }, { "r": "4.5.3", "os": "win", "version": "3.1.0", "date": "2026-09-01T06:42:43.000Z", "commit": "7f006b2a27d0c2c4b2ffbc280585f713db5f6f66", "fileid": "https://r2.ropensci.org/8a8e0d176124fbccb3d2580b8e7fd6bdf201d932ebfcb8837010c77b1d83be1a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/igdawg/actions/runs/33478427788" }, { "r": "4.6.1", "os": "win", "version": "3.1.0", "date": "2026-09-01T06:42:30.000Z", "commit": "7f006b2a27d0c2c4b2ffbc280585f713db5f6f66", "fileid": "https://r2.ropensci.org/56b5232244b904838f98fb8f20764cad9c98fcc14c8a8d2fc9f36ecc4e39f452", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/igdawg/actions/runs/33478427788" }, { "r": "4.7.0", "os": "linux", "version": "3.1.0", "date": "2026-10-01T07:52:23.000Z", "distro": "resolute", "commit": "7f006b2a27d0c2c4b2ffbc280585f713db5f6f66", "fileid": "https://r2.ropensci.org/821112d86ffd8db4e6147472af3717e984a641fc71f9c353679b047fc2c2d247", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/igdawg/actions/runs/36832252777" }, { "r": "4.6.1", "os": "linux", "version": "3.1.0", "date": "2026-10-01T07:52:30.000Z", "distro": "resolute", "commit": "7f006b2a27d0c2c4b2ffbc280585f713db5f6f66", "fileid": "https://r2.ropensci.org/a392359847c21cfcdee4e3d55247dfdb8faec60874e8bee4451c4afe640e5cc0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/igdawg/actions/runs/36832252777" }, { "r": "4.6.0", "os": "wasm", "version": "3.1.0", "date": "2026-10-01T07:52:15.000Z", "commit": "7f006b2a27d0c2c4b2ffbc280585f713db5f6f66", "fileid": "https://r2.ropensci.org/7b8689874a57c63580c479b62865ed1c673eb21a265651c62e4f214c525aee84", "status": "success", "buildurl": "https://github.com/r-universe/igdawg/actions/runs/36832252777" }, { "r": "4.7.0", "os": "win", "version": "3.1.0", "date": "2026-10-01T07:51:01.000Z", "commit": "7f006b2a27d0c2c4b2ffbc280585f713db5f6f66", "fileid": "https://r2.ropensci.org/342b4b7f9eab21fd1fc0cf968eaa8d28c0ba80876f3a5ff060603d4198ae0739", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/igdawg/actions/runs/36832252777" } ] }