{
  "_id": "6a5c68609baadeef8ab4f99b",
  "Package": "CCAFE",
  "Type": "Package",
  "Title": "Case Control Allele Frequency Estimation",
  "Version": "1.5.0",
  "Authors@R": "c(person(\"Hayley\", \"Wolff\", email = \"hayley.wolff@cuanschutz.edu\", role = c(\"cre\", \"aut\")))",
  "Description": "Functions to reconstruct case and control AFs from summary\nstatistics. One function uses OR, NCase, NControl, and\nSE(log(OR)). The second function uses OR, NCase, NControl, and\nAF for the whole sample.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "false",
  "RoxygenNote": "7.3.2",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "URL": "https://github.com/wolffha/CCAFE/",
  "BugReports": "https://github.com/wolffha/CCAFE/issues",
  "biocViews": "GenomeWideAssociation, ComparativeGenomics, Genetics,\nPreprocessing, SNP, Software, WholeGenome",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:04:43 UTC",
  "RemoteUrl": "https://github.com/bioc/CCAFE",
  "RemoteRef": "HEAD",
  "RemoteSha": "1905db01f8cf0620887982570e3161d5b2787cba",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-19 05:55:07 UTC",
    "User": "root"
  },
  "Author": "Hayley Wolff [cre, aut]",
  "Maintainer": "Hayley Wolff <hayley.wolff@cuanschutz.edu>",
  "_user": "bioc",
  "_type": "src",
  "_file": "CCAFE_1.5.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/7e86e78f376f74df105e879cf3e6d66a605a03c72c8073963e041b7166c4806a",
  "_filesize": 5619931,
  "_sha256": "7e86e78f376f74df105e879cf3e6d66a605a03c72c8073963e041b7166c4806a",
  "_expires": "2026-10-27T06:02:06.000Z",
  "_created": "2026-07-19T05:55:07.000Z",
  "_published": "2026-07-19T06:02:08.037Z",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 6
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29675452252",
  "_status": "success",
  "_upstream": "https://github.com/bioc/CCAFE",
  "_commit": {
    "id": "1905db01f8cf0620887982570e3161d5b2787cba",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381483
  },
  "_maintainer": {
    "name": "Hayley Wolff",
    "email": "hayley.wolff@cuanschutz.edu"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 88162345534,
      "time": 190,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8438781793"
    },
    {
      "job": 88162345536,
      "time": 267,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8438793375"
    },
    {
      "job": 88162345580,
      "time": 366,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8438809081"
    },
    {
      "job": 88162345540,
      "time": 163,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8438777687"
    },
    {
      "job": 88162345528,
      "time": 155,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8438776538"
    },
    {
      "job": 88161992911,
      "time": 314,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8438755102"
    },
    {
      "job": 88162345503,
      "time": 182,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8438780621"
    },
    {
      "job": 88162345569,
      "time": 146,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8438775417"
    },
    {
      "job": 88162345565,
      "time": 143,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8438775012"
    },
    {
      "job": 88162345574,
      "time": 159,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8438777642"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4.0",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "VariantAnnotation",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "tidyverse",
      "role": "Suggests"
    },
    {
      "package": "DescTools",
      "role": "Suggests"
    },
    {
      "package": "cowplot",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "GenomicRanges",
      "role": "Suggests"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Suggests"
    },
    {
      "package": "S4Vectors",
      "role": "Suggests"
    },
    {
      "package": "IRanges",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.5.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.4.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "genomewideassociation",
    "comparativegenomics",
    "genetics",
    "preprocessing",
    "snp",
    "software",
    "wholegenome"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "wolffha",
      "count": 106,
      "uuid": 150075196
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 449,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 276,
    "source": "https://www.bioconductor.org/packages/stats/bioc/CCAFE"
  },
  "_devurl": "https://github.com/wolffha/ccafe",
  "_searchresults": 18,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/CCAFE.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/wolffha/ccafe",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "CaseControl_AF",
    "CaseControl_SE",
    "CCAFE_convertVCF"
  ],
  "_datasets": [
    {
      "name": "sampleDat",
      "title": "PanUKBB and gnomAD Diabetes Data",
      "object": "sampleDat",
      "file": "sampleDat.rda",
      "class": [
        "rowwise_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "CHR",
        "POS",
        "REF",
        "ALT",
        "true_maf_case",
        "true_maf_control",
        "beta",
        "SE",
        "gnomad_maf",
        "OR",
        "true_maf_pop"
      ],
      "rows": 500,
      "table": true,
      "tojson": true
    },
    {
      "name": "vcf_sample",
      "title": "A VCF from this GWAS of Type 2 Diabetes https://doi.org/10.1038/s41588-018-0084-1. containing a subset of 10,000 variants",
      "object": "vcf_sample",
      "file": "vcf_sample.rda",
      "class": [
        "CollapsedVCF"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "CaseControl_AF",
      "title": "CaseControl_AF",
      "topics": [
        "CaseControl_AF"
      ]
    },
    {
      "page": "CaseControl_SE",
      "title": "CaseControl_SE",
      "topics": [
        "CaseControl_SE"
      ]
    },
    {
      "page": "CCAFE_convertVCF",
      "title": "CCAFE_convertVCF",
      "topics": [
        "CCAFE_convertVCF"
      ]
    },
    {
      "page": "sampleDat",
      "title": "PanUKBB and gnomAD Diabetes Data",
      "topics": [
        "sampleDat"
      ]
    },
    {
      "page": "vcf_sample",
      "title": "A VCF from this GWAS of Type 2 Diabetes https://doi.org/10.1038/s41588-018-0084-1. containing a subset of 10,000 variants",
      "topics": [
        "vcf_sample"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/CCAFE/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "cachem",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "DelayedArray",
    "dplyr",
    "fastmap",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "glue",
    "httr",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "R6",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyselect",
    "utf8",
    "VariantAnnotation",
    "vctrs",
    "withr",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "CCAFE_Extra_Details.Rmd",
      "filename": "CCAFE_Extra_Details.html",
      "title": "CCAFE Extra Details",
      "author": "Hayley Stoneman",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Simulated dataset",
        "MAF vs AF",
        "Minor alleles in CaseControl_SE",
        "Examples in simulated data",
        "Using total minor allele frequency in CaseControl_AF",
        "Demonstration in simulations",
        "Variants on sex chromosomes",
        "Session Info"
      ],
      "created": "2024-10-02 20:37:08",
      "modified": "2025-03-10 23:23:22",
      "commits": 3
    },
    {
      "source": "CCAFE.Rmd",
      "filename": "CCAFE.html",
      "title": "CCAFE Vignette",
      "author": "Hayley Stoneman",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Overview of CCAFE Functions",
        "CaseControl_AF",
        "CaseControl_AF() input",
        "CaseControl_AF() output",
        "CaseControl_SE",
        "CaseControl_SE() input",
        "CaseControl_SE() output",
        "Examples",
        "A quick demo of CaseControl_AF()",
        "A quick demo of CaseControl_SE()",
        "Integration with Bioconductor",
        "Tabular data",
        "VCF data",
        "VCF Conversion Function",
        "Session Information"
      ],
      "created": "2024-10-02 20:37:08",
      "modified": "2025-03-10 23:23:22",
      "commits": 10
    }
  ],
  "_score": 4.556302500767288,
  "_indexed": true,
  "_nocasepkg": "ccafe",
  "_universes": [
    "bioc",
    "wolffha"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.5.0",
      "date": "2026-07-19T05:59:00.000Z",
      "distro": "resolute",
      "commit": "1905db01f8cf0620887982570e3161d5b2787cba",
      "fileid": "https://r2.ropensci.org/91faf47eadbdfb92c3c7b5c310628c2f6443a713a96f17f6ddef4d92c6e23e83",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675452252"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.5.0",
      "date": "2026-07-19T06:00:30.000Z",
      "distro": "resolute",
      "commit": "1905db01f8cf0620887982570e3161d5b2787cba",
      "fileid": "https://r2.ropensci.org/a1968f44b3e2d3b25c1e327c2eb5253a47941df7aab53330787eca317175b9da",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675452252"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.5.0",
      "date": "2026-07-19T05:57:12.000Z",
      "commit": "1905db01f8cf0620887982570e3161d5b2787cba",
      "fileid": "https://r2.ropensci.org/02f59d2b0e7195a08e06fa3191b87a223f671c9015975291c21d2281eeabbc9c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675452252"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.5.0",
      "date": "2026-07-19T05:57:13.000Z",
      "commit": "1905db01f8cf0620887982570e3161d5b2787cba",
      "fileid": "https://r2.ropensci.org/00af876ed345ad218324269dbfe6df1084f90bd64c3ed6141b0459552e986385",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675452252"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.5.0",
      "date": "2026-07-19T05:58:32.000Z",
      "commit": "1905db01f8cf0620887982570e3161d5b2787cba",
      "fileid": "https://r2.ropensci.org/202ca813218742c14c66ec410e6c32d5c54e03a6818fc8dd4ecda530976e5670",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675452252"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.5.0",
      "date": "2026-07-19T05:56:50.000Z",
      "commit": "1905db01f8cf0620887982570e3161d5b2787cba",
      "fileid": "https://r2.ropensci.org/964758b1b97f7d7881e75b9859798839a380ce996cec0a74dab3fedfca078efe",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675452252"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.5.0",
      "date": "2026-07-19T05:56:49.000Z",
      "commit": "1905db01f8cf0620887982570e3161d5b2787cba",
      "fileid": "https://r2.ropensci.org/52bbdfd823c920e5739614c1424a9d11f98f80d10a90b2af1b8f0850200c1b9c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675452252"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.5.0",
      "date": "2026-07-19T05:57:08.000Z",
      "commit": "1905db01f8cf0620887982570e3161d5b2787cba",
      "fileid": "https://r2.ropensci.org/8f2efb11c5fe1133048850e0f6ad1a0939de2febfcf39c60e4c8d2ff3dec1ec3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29675452252"
    }
  ]
}