{
  "_id": "6a1ed4d4b401979e7340e382",
  "Package": "fcfdr",
  "Title": "Flexible cFDR",
  "Version": "1.0.0",
  "Authors@R": "c(person(given = \"Anna\",\nfamily = \"Hutchinson\",\nrole = c(\"aut\", \"cre\"),\nemail = \"annahutchinson1995@gmail.com\",\ncomment = c(ORCID = \"0000-0002-9224-4410\")),\nperson(\"Chris\", \"Wallace\", role = c(\"aut\")),\nperson(\"Thomas\",\"Willis\", role = c(\"ctb\", \"aut\")),\nperson(\"James\", \"Liley\", role = c(\"ctb\")))",
  "Description": "Provides functions to implement the Flexible cFDR\n(Hutchinson et al. (2021) <doi:10.1371/journal.pgen.1009853>)\nand Binary cFDR (Hutchinson et al. (2021)\n<doi:10.1101/2021.10.21.465274>) methodologies to leverage\nauxiliary data from arbitrary distributions, for example\nfunctional genomic data, with GWAS p-values to generate\nre-weighted p-values.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.1.2",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-20 10:53:18 UTC",
    "User": "root"
  },
  "Author": "Anna Hutchinson [aut, cre]\n(<https://orcid.org/0000-0002-9224-4410>), Chris Wallace [aut],\nThomas Willis [ctb, aut], James Liley [ctb]",
  "Maintainer": "Anna Hutchinson <annahutchinson1995@gmail.com>",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev",
  "Repository": "https://annahutch.r-universe.dev",
  "Date/Publication": "2022-02-08 10:25:10 UTC",
  "RemoteUrl": "https://github.com/annahutch/fcfdr",
  "RemoteRef": "HEAD",
  "RemoteSha": "c2e73698a179726dadf2b28b07b121a4cdc6aa40",
  "MD5sum": "0ea265eb0fc9162b7e01dcfca635c01c",
  "_user": "annahutch",
  "_type": "src",
  "_file": "fcfdr_1.0.0.tar.gz",
  "_fileid": "97ae24dfcf8892a2bbe97f4c39db04541a5f9de5fcc907b078f57c7e23e2ba0d",
  "_filesize": 5500655,
  "_sha256": "97ae24dfcf8892a2bbe97f4c39db04541a5f9de5fcc907b078f57c7e23e2ba0d",
  "_created": "2026-05-20T10:53:18.000Z",
  "_published": "2026-06-02T13:04:20.452Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79076852149,
      "time": 193,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7108071104"
    },
    {
      "job": 79076852489,
      "time": 178,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7108066220"
    },
    {
      "job": 79076852815,
      "time": 112,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7108045927"
    },
    {
      "job": 79076852217,
      "time": 129,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7108050660"
    },
    {
      "job": 79076851570,
      "time": 964,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7108010284"
    },
    {
      "job": 79076851683,
      "time": 133,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7358438443"
    },
    {
      "job": 79076852102,
      "time": 171,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7108064364"
    },
    {
      "job": 79076852776,
      "time": 144,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7108055083"
    },
    {
      "job": 79076852219,
      "time": 129,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7108051053"
    }
  ],
  "_buildurl": "https://github.com/r-universe/annahutch/actions/runs/26157142461",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/annahutch/fcfdr",
  "_commit": {
    "id": "c2e73698a179726dadf2b28b07b121a4cdc6aa40",
    "author": "Anna Hutchinson <42926930+annahutch@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #8 from annahutch/website\n\nWebpage push to github",
    "time": 1644315910
  },
  "_maintainer": {
    "name": "Anna Hutchinson",
    "email": "annahutchinson1995@gmail.com",
    "login": "annahutch",
    "description": "",
    "uuid": 42926930,
    "orcid": "0000-0002-9224-4410"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "locfdr",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "fields",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "spatstat.geom",
      "role": "Imports"
    },
    {
      "package": "polyCub",
      "role": "Imports"
    },
    {
      "package": "hexbin",
      "role": "Imports"
    },
    {
      "package": "bigsplines",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "Hmisc",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "digest",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "annahutch",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 6,
  "_contributors": [
    {
      "user": "annahutch",
      "count": 99,
      "uuid": 42926930
    },
    {
      "user": "twillis209",
      "count": 16,
      "uuid": 30097448
    },
    {
      "user": "chr1swallace",
      "count": 1,
      "uuid": 2189544
    }
  ],
  "_userbio": {
    "uuid": 42926930,
    "type": "user",
    "name": "Anna Hutchinson"
  },
  "_downloads": {
    "count": 231,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/fcfdr"
  },
  "_devurl": "https://github.com/annahutch/fcfdr",
  "_searchresults": 9,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/fcfdr.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/annahutch/fcfdr",
  "_realowner": "annahutch",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2022-02-07"
    }
  ],
  "_exports": [
    "binary_cfdr",
    "corr_plot",
    "flexible_cfdr",
    "log10pv_plot",
    "parameters_in_locfdr",
    "pv_plot",
    "stratified_qqplot"
  ],
  "_datasets": [
    {
      "name": "T1D_application_data",
      "title": "Data for T1D application",
      "object": "T1D_application_data",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "rsID",
        "CHR19",
        "BP19",
        "REF",
        "ALT",
        "T1D_pval",
        "MAF",
        "LDAK_weight",
        "RA_pval",
        "DGF",
        "H3K27ac"
      ],
      "rows": 113543,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "binary_cfdr",
      "title": "Perform cFDR leveraging binary auxiliary covariates",
      "topics": [
        "binary_cfdr"
      ]
    },
    {
      "page": "corr_plot",
      "title": "Violin plot of p-values for quantiles of q",
      "topics": [
        "corr_plot"
      ]
    },
    {
      "page": "flexible_cfdr",
      "title": "Perform Flexible cFDR",
      "topics": [
        "flexible_cfdr"
      ]
    },
    {
      "page": "log10pv_plot",
      "title": "Plot -log10(p) against -log10(v) and colour by q",
      "topics": [
        "log10pv_plot"
      ]
    },
    {
      "page": "match_ind_maf",
      "title": "Function to downsample independent SNPs to match MAF distribution of whole set.",
      "topics": [
        "match_ind_maf"
      ]
    },
    {
      "page": "parameters_in_locfdr",
      "title": "parameters_in_locfdr",
      "topics": [
        "parameters_in_locfdr"
      ]
    },
    {
      "page": "pv_plot",
      "title": "Plot p against v and colour by q",
      "topics": [
        "pv_plot"
      ]
    },
    {
      "page": "stratified_qqplot",
      "title": "Stratified Q-Q plot.",
      "topics": [
        "stratified_qqplot"
      ]
    },
    {
      "page": "T1D_application_data",
      "title": "Data for T1D application",
      "topics": [
        "T1D_application_data"
      ]
    }
  ],
  "_pkglogo": "https://github.com/annahutch/fcfdr/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/annahutch/fcfdr/raw/HEAD/README.md",
  "_rundeps": [
    "backports",
    "base64enc",
    "bigsplines",
    "bslib",
    "cachem",
    "checkmate",
    "cli",
    "cluster",
    "colorspace",
    "cowplot",
    "cpp11",
    "data.table",
    "deldir",
    "digest",
    "dotCall64",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "fields",
    "fontawesome",
    "foreign",
    "Formula",
    "fs",
    "generics",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "hexbin",
    "highr",
    "Hmisc",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "isoband",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lattice",
    "lifecycle",
    "locfdr",
    "magrittr",
    "maps",
    "MASS",
    "Matrix",
    "memoise",
    "mime",
    "nnet",
    "pillar",
    "pkgconfig",
    "polyclip",
    "polyCub",
    "quadprog",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "rmarkdown",
    "rpart",
    "rstudioapi",
    "S7",
    "sass",
    "scales",
    "sp",
    "spam",
    "spatstat.data",
    "spatstat.geom",
    "spatstat.univar",
    "spatstat.utils",
    "stringi",
    "stringr",
    "tibble",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "extra-information.Rmd",
      "filename": "extra-information.html",
      "title": "Extra Information",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Contents",
        "Genomic control",
        "Auxiliary data",
        "Finding independent subsets of SNPs",
        "Applying cFDR iteratively"
      ],
      "created": "2020-11-16 13:28:50",
      "modified": "2022-02-07 17:10:48",
      "commits": 4
    },
    {
      "source": "fcfdr-vignette.Rmd",
      "filename": "fcfdr-vignette.html",
      "title": "Introductory vignette",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Simple walk-through example"
      ],
      "created": "2020-09-21 16:55:16",
      "modified": "2022-02-08 10:25:10",
      "commits": 10
    },
    {
      "source": "ldak-vignette.Rmd",
      "filename": "ldak-vignette.html",
      "title": "LDAK vignette",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Optional: Obtaining and processing the 1000G data",
        "Joining the 1000G and GWAS SNPs",
        "Running the LDAK weighting calculation procedure",
        "Using the LDAK weightings in flexible_fcfdr"
      ],
      "created": "2021-04-21 20:20:47",
      "modified": "2022-02-07 17:10:48",
      "commits": 4
    },
    {
      "source": "t1d_app.Rmd",
      "filename": "t1d_app.html",
      "title": "T1D Application",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2020-10-19 13:13:54",
      "modified": "2022-02-08 10:25:10",
      "commits": 20
    }
  ],
  "_score": 5.380211241711606,
  "_indexed": true,
  "_nocasepkg": "fcfdr",
  "_universes": [
    "annahutch"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-05-20T10:55:53.000Z",
      "distro": "noble",
      "commit": "c2e73698a179726dadf2b28b07b121a4cdc6aa40",
      "fileid": "ecf6e9db46ab00b15bc1ec853cd9a15fc61c6dc4ee085bae0c217d625b677afe",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/annahutch/actions/runs/26157142461"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-05-20T10:55:50.000Z",
      "distro": "noble",
      "commit": "c2e73698a179726dadf2b28b07b121a4cdc6aa40",
      "fileid": "aaf5d07240d63a16c77f83f9ea059d355b53efcedd0562cbe54f0cb9b2d88d71",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/annahutch/actions/runs/26157142461"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-05-20T10:54:54.000Z",
      "commit": "c2e73698a179726dadf2b28b07b121a4cdc6aa40",
      "fileid": "2db82054e7218e8db2bfa41232f2e7160c34f2f58b4c1c931b281296afa51c38",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/annahutch/actions/runs/26157142461"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-05-20T10:55:06.000Z",
      "commit": "c2e73698a179726dadf2b28b07b121a4cdc6aa40",
      "fileid": "f3d6dabf69621fea5a35ea3b20233948d5e18f7ae7e1fa8a5ca05cb58ae40a4e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/annahutch/actions/runs/26157142461"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-05-20T10:54:57.000Z",
      "commit": "c2e73698a179726dadf2b28b07b121a4cdc6aa40",
      "fileid": "61b0843e4cb503366c576a73bf06b4cc75f24fff75b28b8ac40d0a6c6d57314f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/annahutch/actions/runs/26157142461"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-05-20T10:55:02.000Z",
      "commit": "c2e73698a179726dadf2b28b07b121a4cdc6aa40",
      "fileid": "732c16fdf6e8dcc556dbd75f675fbc611e378325fca3e693dc457705c8ebbc0a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/annahutch/actions/runs/26157142461"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-05-20T10:54:46.000Z",
      "commit": "c2e73698a179726dadf2b28b07b121a4cdc6aa40",
      "fileid": "8ebcfcaf54dd87158c1044a0be8482970a01fda19f787370c2b4c57c0213f3d2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/annahutch/actions/runs/26157142461"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.0",
      "date": "2026-06-02T13:03:53.000Z",
      "commit": "c2e73698a179726dadf2b28b07b121a4cdc6aa40",
      "fileid": "22c0b5dba81469b4ee2ef961d59eee667d7e521fe25edba383dbd340871b5283",
      "status": "success",
      "buildurl": "https://github.com/r-universe/annahutch/actions/runs/26157142461"
    }
  ]
}