{ "_id": "6aba187c99f7aa8c6aa3c40f", "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", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-27 18:41:44 UTC", "User": "root" }, "Author": "Derek Pappas [aut], Livia Tran [aut], Steve Mack [aut, cre],\nJill Hollenbach [aut]", "Config/pak/sysreqs": "libxml2-dev", "Repository": "https://cranhaven.r-universe.dev", "Date/Publication": "2026-09-27 08:02:00 UTC", "RemoteUrl": "https://github.com/cranhaven/cranhaven.r-universe.dev", "RemoteRef": "package/BIGDAWG", "RemoteSha": "16718317b25508ccf6fe79ed0a3c0546614f0ad0", "RemoteSubdir": "BIGDAWG", "_user": "cranhaven", "_type": "src", "_file": "BIGDAWG_3.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/bd9b5ec706d357c7e70e076aa4403f0a8752cff21e2728d4157f7301e6aab0bf", "_filesize": 1340203, "_sha256": "bd9b5ec706d357c7e70e076aa4403f0a8752cff21e2728d4157f7301e6aab0bf", "_expires": "2027-01-05T19:05:22.000Z", "_created": "2026-09-27T18:41:44.000Z", "_published": "2026-09-28T07:34:20.224Z", "_jobs": [ { "job": 108825605248, "time": 164, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10939003059" }, { "job": 108825605057, "time": 136, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10938739403" }, { "job": 108825603776, "time": 149, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10956119087" }, { "job": 108825603729, "time": 113, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10956583827" }, { "job": 108825604869, "time": 234, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10939295630" }, { "job": 108825605318, "time": 129, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10938898386" }, { "job": 108825605602, "time": 122, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10939315808" }, { "job": 108825606035, "time": 84, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10939605157" }, { "job": 108825605947, "time": 95, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10939610143" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/cranhaven/actions/runs/36341329977", "_status": "success", "_upstream": "https://github.com/cranhaven/cranhaven.r-universe.dev", "_commit": { "id": "16718317b25508ccf6fe79ed0a3c0546614f0ad0", "author": "GitHub Action ", "committer": "GitHub Action ", "message": "Add BIGDAWG to CRANhaven, because archived on 2026-09-27 08:02:00 +0000\n", "time": 1790496120 }, "_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": "cranhaven", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2026-39", "n": 1 } ], "_tags": [], "_topics": [ "archived", "packages", "r-universe" ], "_stars": 5, "_contributors": [ { "user": "henrikbengtsson", "count": 183, "uuid": 1616850 } ], "_userbio": { "uuid": 161993010, "type": "organization", "name": "cranhaven", "followers": 3, "description": "CRANhaven - Repository for Recently Archived CRAN Packages" }, "_downloads": { "count": 621, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BIGDAWG" }, "_mentions": 7, "_devurl": "https://github.com/igdawg/bigdawg", "_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" ], "_homeurl": "https://github.com/igdawg/bigdawg", "_realowner": "igdawg", "_cranurl": false, "_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": [ { "page": "A", "title": "Amino Acid Analysis Function", "topics": [ "A" ] }, { "page": "A.wrapper", "title": "Amino Acid Wrapper", "topics": [ "A.wrapper" ] }, { "page": "AA.df.check", "title": "Contingency Table Check", "topics": [ "AA.df.check" ] }, { "page": "AA.df.cs", "title": "Contingency Table Amino Acid ChiSq Testing", "topics": [ "AA.df.cs" ] }, { "page": "AAtable.builder", "title": "Amino Acid Contingency Table Build", "topics": [ "AAtable.builder" ] }, { "page": "AlignmentFilter", "title": "Alignment Filter", "topics": [ "AlignmentFilter" ] }, { "page": "AlignObj.Create", "title": "Alignment Object Creator", "topics": [ "AlignObj.Create" ] }, { "page": "AlignObj.Update", "title": "Updated Alignment Object Creator", "topics": [ "AlignObj.Update" ] }, { "page": "Append.System", "title": "Append Genetic System Locus Designation to Allele String", "topics": [ "Append.System" ] }, { "page": "BIGDAWG", "title": "BIGDAWG Main Wrapper Function v1.1 Livia Tran March 26, 2026", "topics": [ "BIGDAWG" ] }, { "page": "Build.Matrix", "title": "Build Output Matrix for GL2Tab Conversion", "topics": [ "Build.Matrix" ] }, { "page": "buildHAPnames", "title": "Haplotype Name Builder", "topics": [ "buildHAPnames" ] }, { "page": "buildHAPsets", "title": "Haplotype List Builder", "topics": [ "buildHAPsets" ] }, { "page": "cci", "title": "Case-Control Odds ratio calculation and graphing", "topics": [ "cci" ] }, { "page": "cci.pval", "title": "Case Control Odds Ratio Calculation from Epicalc", "topics": [ "cci.pval" ] }, { "page": "cci.pval.list", "title": "Case Control Odds Ratio Calculation from Epicalc list variation", "topics": [ "cci.pval.list" ] }, { "page": "Check.Cores", "title": "Check Cores Parameters", "topics": [ "Check.Cores" ] }, { "page": "Check.Data", "title": "Check Data Structure", "topics": [ "Check.Data" ] }, { "page": "Check.Params", "title": "Check Input Parameters", "topics": [ "Check.Params" ] }, { "page": "Check.Params.GLS", "title": "Check Input Parameters for GLS conversion", "topics": [ "Check.Params.GLS" ] }, { "page": "CheckAlleles", "title": "HLA Allele Legitimacy Check for Amino Acid Analysis", "topics": [ "CheckAlleles" ] }, { "page": "CheckHLA", "title": "HLA Formatting Check for Amino Acid Analysis", "topics": [ "CheckHLA" ] }, { "page": "CheckLoci", "title": "HLA Loci Legitimacy Check for Amino Acid Analysis", "topics": [ "CheckLoci" ] }, { "page": "CheckRelease", "title": "Function to Check Release Versions", "topics": [ "CheckRelease" ] }, { "page": "CheckString.Allele", "title": "GL String Allele Check", "topics": [ "CheckString.Allele" ] }, { "page": "CheckString.Locus", "title": "GL String Locus Check", "topics": [ "CheckString.Locus" ] }, { "page": "Condense.EPL", "title": "Condensing Exon Specific Alignments to Single Dataframe", "topics": [ "Condense.EPL" ] }, { "page": "Create.Null.Table", "title": "Create Empty Table", "topics": [ "Create.Null.Table" ] }, { "page": "DRB345.Check.Wrapper", "title": "DRB345 haplotype zygosity wrapper", "topics": [ "DRB345.Check.Wrapper" ] }, { "page": "DRB345.Check.Zygosity", "title": "DRB345 haplotype zygosity checker single locus", "topics": [ "DRB345.Check.Zygosity" ] }, { "page": "DRB345.Exp", "title": "DRB345 Expected", "topics": [ "DRB345.Exp" ] }, { "page": "DRB345.parser", "title": "DRB345 Column Processing", "topics": [ "DRB345.parser" ] }, { "page": "Err.Log", "title": "Error Code Display and Logging", "topics": [ "Err.Log" ] }, { "page": "EVSremoval", "title": "Expression Variant Suffix Removal", "topics": [ "EVSremoval" ] }, { "page": "Exon.Filter", "title": "Filter Exon Specific Alignment Sections", "topics": [ "Exon.Filter" ] }, { "page": "ExonPtnAlign.Create", "title": "Protein Exon Alignment Formatter", "topics": [ "ExonPtnAlign.Create" ] }, { "page": "ExonPtnList", "title": "Exon protein alignments.", "topics": [ "ExonPtnList" ] }, { "page": "Filler", "title": "Replace or Fill 00:00 allele strings", "topics": [ "Filler" ] }, { "page": "Format.Allele", "title": "Ambiguous Alleles Locus Name Formatting", "topics": [ "Format.Allele" ] }, { "page": "Format.Tab", "title": "Tabular Data Locus Format Tool", "topics": [ "Format.Tab" ] }, { "page": "getAllele.Count", "title": "Recompute number of alleles", "topics": [ "getAllele.Count" ] }, { "page": "getCS.Mat", "title": "Chi square matrices", "topics": [ "getCS.Mat" ] }, { "page": "getCS.stat", "title": "Chi square test statistic", "topics": [ "getCS.stat" ] }, { "page": "GetField", "title": "HLA trimming function", "topics": [ "GetField" ] }, { "page": "getFileName", "title": "File Name Extraction", "topics": [ "getFileName" ] }, { "page": "GetFiles", "title": "File Fetcher", "topics": [ "GetFiles" ] }, { "page": "getHap", "title": "Haplotype Table Maker", "topics": [ "getHap" ] }, { "page": "getObsFreq", "title": "Observed Frequency", "topics": [ "getObsFreq" ] }, { "page": "GL2Tab.Loci", "title": "Locus Ordering for GL2Tab", "topics": [ "GL2Tab.Loci" ] }, { "page": "GL2Tab.Sub", "title": "Genotype List String Expander", "topics": [ "GL2Tab.Sub" ] }, { "page": "GL2Tab.wrapper", "title": "Genotype List String to Tabular Data Conversion", "topics": [ "GL2Tab.wrapper" ] }, { "page": "GLSconvert", "title": "Genotype List String Conversion", "topics": [ "GLSconvert" ] }, { "page": "H.MC", "title": "Haplotype Analysis Function for Multicore", "topics": [ "H.MC" ] }, { "page": "H.MC.wrapper", "title": "Haplotype Wrapper for Multicore", "topics": [ "H.MC.wrapper" ] }, { "page": "HLA_data", "title": "Example HLA Dataset", "topics": [ "HLA_data" ] }, { "page": "HWE", "title": "Hardy Weinbergy Equilibrium Function", "topics": [ "HWE" ] }, { "page": "HWE.ChiSq", "title": "Hardy Weinbergy Equilibrium Function", "topics": [ "HWE.ChiSq" ] }, { "page": "HWE.wrapper", "title": "Hardy-Weinbery Wrapper", "topics": [ "HWE.wrapper" ] }, { "page": "L", "title": "Locus Analysis Function 25Jun2025", "topics": [ "L" ] }, { "page": "L.wrapper", "title": "Locus Wrapper", "topics": [ "L.wrapper" ] }, { "page": "make2x2", "title": "Creation of a 2x2 table using the indicated orientation.", "topics": [ "make2x2" ] }, { "page": "makeComb", "title": "Genotype Combination Maker", "topics": [ "makeComb" ] }, { "page": "MergeData_Output", "title": "Data Object Merge and Output", "topics": [ "MergeData_Output" ] }, { "page": "PgrpExtract", "title": "HLA P group Finder", "topics": [ "PgrpExtract" ] }, { "page": "PgrpFormat", "title": "HLA P group File Formatter", "topics": [ "PgrpFormat" ] }, { "page": "PreCheck", "title": "Data Summary Function", "topics": [ "PreCheck" ] }, { "page": "prepData", "title": "Prepare imported data v 1.1 10 December 2025", "topics": [ "prepData" ] }, { "page": "rmABstrings", "title": "Replace absent allele strings", "topics": [ "rmABstrings" ] }, { "page": "RunChiSq", "title": "Strict Chi-squared Contingency Table Test", "topics": [ "RunChiSq" ] }, { "page": "RunChiSq_c", "title": "Contextual Binning Chi-squared Contingency Table Test", "topics": [ "RunChiSq_c" ] }, { "page": "Stripper", "title": "Removes System and Locus from Alleles", "topics": [ "Stripper" ] }, { "page": "summaryGeno.2", "title": "Haplotype missing Allele summary function", "topics": [ "summaryGeno.2" ] }, { "page": "Tab2GL.Loci", "title": "Locus Condenser for Tab2GL", "topics": [ "Tab2GL.Loci" ] }, { "page": "Tab2GL.Sub", "title": "Genotype List String Condenser", "topics": [ "Tab2GL.Sub" ] }, { "page": "Tab2GL.wrapper", "title": "Genotype List String to Tabular Data Conversion", "topics": [ "Tab2GL.wrapper" ] }, { "page": "TableMaker", "title": "Table Maker", "topics": [ "TableMaker" ] }, { "page": "UpdateRelease", "title": "Update function for protein aligment upon new IMGT HLA data release", "topics": [ "UpdateRelease" ] } ], "_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": "2026-09-27 08:02:00", "modified": "2026-09-27 08:02:00", "commits": 1 }, { "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": "2026-09-27 08:02:00", "modified": "2026-09-27 08:02:00", "commits": 1 } ], "_score": 4.3222192947339195, "_indexed": false, "_nocasepkg": "bigdawg", "_universes": [ "cranhaven" ], "_indexurl": "https://igdawg.r-universe.dev/BIGDAWG", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.1.0", "date": "2026-09-27T18:44:15.000Z", "distro": "resolute", "commit": "16718317b25508ccf6fe79ed0a3c0546614f0ad0", "fileid": "https://r2.ropensci.org/3946d87e326c3920b01d9805b21f8a0c6af4899d1282037cdbe31acbf82bf312", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cranhaven/actions/runs/36341329977" }, { "r": "4.6.1", "os": "linux", "version": "3.1.0", "date": "2026-09-27T18:44:02.000Z", "distro": "resolute", "commit": "16718317b25508ccf6fe79ed0a3c0546614f0ad0", "fileid": "https://r2.ropensci.org/093925b7574352911481c56796202ce117e1879a4bc64c6400721d6c462c26f2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cranhaven/actions/runs/36341329977" }, { "r": "4.5.3", "os": "mac", "version": "3.1.0", "date": "2026-09-28T07:33:03.000Z", "commit": "16718317b25508ccf6fe79ed0a3c0546614f0ad0", "fileid": "https://r2.ropensci.org/4b1f04f2c367a405702c6409cabc2783a3a6086ca408fb4fd2d615ec2c78479d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cranhaven/actions/runs/36341329977" }, { "r": "4.6.1", "os": "mac", "version": "3.1.0", "date": "2026-09-28T07:32:39.000Z", "commit": "16718317b25508ccf6fe79ed0a3c0546614f0ad0", "fileid": "https://r2.ropensci.org/edb75634fa97e2b903c415ebe5c9a92758c994fd0b0443e311163cf5e33e1acf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cranhaven/actions/runs/36341329977" }, { "r": "4.6.0", "os": "wasm", "version": "3.1.0", "date": "2026-09-27T18:44:12.000Z", "commit": "16718317b25508ccf6fe79ed0a3c0546614f0ad0", "fileid": "https://r2.ropensci.org/853722da59c6476d3f067bc91fbadff3c36a491faaf603b0a6c30848a514fd0b", "status": "success", "buildurl": "https://github.com/r-universe/cranhaven/actions/runs/36341329977" }, { "r": "4.7.0", "os": "win", "version": "3.1.0", "date": "2026-09-27T18:43:24.000Z", "commit": "16718317b25508ccf6fe79ed0a3c0546614f0ad0", "fileid": "https://r2.ropensci.org/1075ef8978ac35a8047d89396e4e6debc3268aa5eb5b11f0fb15493244252a67", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cranhaven/actions/runs/36341329977" }, { "r": "4.5.3", "os": "win", "version": "3.1.0", "date": "2026-09-27T18:42:57.000Z", "commit": "16718317b25508ccf6fe79ed0a3c0546614f0ad0", "fileid": "https://r2.ropensci.org/550bae0f906b29a841b4668393bb3775995947b4606ac396dd343351dba8169b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cranhaven/actions/runs/36341329977" }, { "r": "4.6.1", "os": "win", "version": "3.1.0", "date": "2026-09-27T18:43:04.000Z", "commit": "16718317b25508ccf6fe79ed0a3c0546614f0ad0", "fileid": "https://r2.ropensci.org/586a8ac5c1605f2ddfa0de697cebc78440d8411d412dfff6fa30f414b7f267db", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cranhaven/actions/runs/36341329977" } ] }