{ "_id": "6ab26e663d719c1f8408d82c", "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": "2026-09-22 11:56:32 UTC", "User": "root" }, "Author": "Hayley Wolff [cre, aut]", "Maintainer": "Hayley Wolff ", "_user": "bioc", "_type": "src", "_file": "CCAFE_1.5.0.tar.gz", "_fileid": "https://r2.ropensci.org/ea062bd0363a5b2c439676e41dc91e945a6ee91950d056c3fb65e1aa584d3df3", "_filesize": 5621384, "_sha256": "ea062bd0363a5b2c439676e41dc91e945a6ee91950d056c3fb65e1aa584d3df3", "_expires": "2026-12-31T12:02:43.000Z", "_created": "2026-09-22T11:56:32.000Z", "_published": "2026-09-22T12:02:46.387Z", "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/35723784629", "_status": "success", "_upstream": "https://github.com/bioc/CCAFE", "_commit": { "id": "1905db01f8cf0620887982570e3161d5b2787cba", "author": "A Wokaty ", "committer": "A Wokaty ", "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": 106734234509, "time": 193, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "10693315890" }, { "job": 106734234390, "time": 311, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10692686400" }, { "job": 106734234492, "time": 253, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10693420951" }, { "job": 106734234483, "time": 111, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10693320634" }, { "job": 106734234400, "time": 148, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10693360693" }, { "job": 106732592178, "time": 324, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10692560904" }, { "job": 106734234501, "time": 165, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10693205872" }, { "job": 106734234556, "time": 139, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10692711032" }, { "job": 106734234510, "time": 168, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10693036032" }, { "job": 106734234549, "time": 152, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10692895862" } ], "_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": 468, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 310, "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/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_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": "2026-09-22T12:01:12.000Z", "distro": "resolute", "commit": "1905db01f8cf0620887982570e3161d5b2787cba", "fileid": "https://r2.ropensci.org/2de11d5808b599a19cb3204f231b05fdb22705cde0250a7aa4f9649377c4e9fa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35723784629" }, { "r": "4.6.1", "os": "linux", "version": "1.5.0", "date": "2026-09-22T12:00:17.000Z", "distro": "resolute", "commit": "1905db01f8cf0620887982570e3161d5b2787cba", "fileid": "https://r2.ropensci.org/4554853ac2a566192fdecd2cf039bb6173b78457b9cd1ca1cc842ac3589f4d01", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35723784629" }, { "r": "4.5.3", "os": "mac", "version": "1.5.0", "date": "2026-09-22T11:58:19.000Z", "commit": "1905db01f8cf0620887982570e3161d5b2787cba", "fileid": "https://r2.ropensci.org/3d5bf5d20c4e4cf02e1c698a4e6a5198e519593359d1fb2815439b23eb5db243", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35723784629" }, { "r": "4.6.1", "os": "mac", "version": "1.5.0", "date": "2026-09-22T11:58:50.000Z", "commit": "1905db01f8cf0620887982570e3161d5b2787cba", "fileid": "https://r2.ropensci.org/d4285d4666ad037e8f42a4616976e3a92f0122be57445162257e56cef6b52ab6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35723784629" }, { "r": "4.6.0", "os": "wasm", "version": "1.5.0", "date": "2026-09-22T11:59:47.000Z", "commit": "1905db01f8cf0620887982570e3161d5b2787cba", "fileid": "https://r2.ropensci.org/e6f60dcdb94d3df2d8a8d8aeef79465d2ca916a44d6ab1f4253a098331494d0e", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35723784629" }, { "r": "4.7.0", "os": "win", "version": "1.5.0", "date": "2026-09-22T11:58:12.000Z", "commit": "1905db01f8cf0620887982570e3161d5b2787cba", "fileid": "https://r2.ropensci.org/73731456d092557f09c833cd6d5376ee25b8918a816caec30b26e0df7497fdae", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35723784629" }, { "r": "4.5.3", "os": "win", "version": "1.5.0", "date": "2026-09-22T11:58:47.000Z", "commit": "1905db01f8cf0620887982570e3161d5b2787cba", "fileid": "https://r2.ropensci.org/1994878f9703cbc274e0a7035712fc48f4d3133faab1b540efacb7791d1ba002", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35723784629" }, { "r": "4.6.1", "os": "win", "version": "1.5.0", "date": "2026-09-22T11:58:32.000Z", "commit": "1905db01f8cf0620887982570e3161d5b2787cba", "fileid": "https://r2.ropensci.org/8c3e655548d4a9c45ce4ae44b8931185bdd61eae82edbe77537d572b79a8bba2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35723784629" } ] }