{
  "_id": "6ad7c57e69e274306bae8987",
  "Package": "sffdr",
  "Type": "Package",
  "Title": "Surrogate Functional False Discovery Rates for Genome-Wide\nAssociation Studies",
  "Version": "1.1.4",
  "Authors@R": "c(person(\"Andrew\", \"Bass\", email =\"ab3105@cam.ac.uk\", role = c(\"aut\", \"cre\")),\nperson(\"Chris\", \"Wallace\", email =\"chris.wallace@cam.ac.uk\", role = c(\"aut\")))",
  "Maintainer": "Andrew Bass <ab3105@cam.ac.uk>",
  "Description": "Pleiotropy-informed significance analysis of genome-wide\nassociation studies with surrogate functional false discovery\nrates (sfFDR). The sfFDR framework adapts the fFDR to leverage\ninformative data from multiple sets of GWAS summary statistics\nto increase power in study while accommodating for linkage\ndisequilibrium. sfFDR provides estimates of key FDR quantities\nin a significance analysis such as the functional local FDR and\n$q$-value, and uses these estimates to derive a functional\n$p$-value for type I error rate control and a functional local\nBayes' factor for post-GWAS analyses (e.g., fine mapping and\ncolocalization).",
  "URL": "https://github.com/ajbass/sffdr",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "LazyData": "true",
  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://ajbass.r-universe.dev",
  "Date/Publication": "2026-10-20 18:45:47 UTC",
  "RemoteUrl": "https://github.com/ajbass/sffdr",
  "RemoteRef": "HEAD",
  "RemoteSha": "0153e7017651b06798bf01f40087ebfe4a04c219",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-20 19:39:30 UTC",
    "User": "root"
  },
  "Author": "Andrew Bass [aut, cre],\nChris Wallace [aut]",
  "_user": "ajbass",
  "_type": "src",
  "_file": "sffdr_1.1.4.tar.gz",
  "_fileid": "https://r2.ropensci.org/cc10832e2910323345e018240878404fcf073f6c23456bade1c09bedaf83d322",
  "_filesize": 639816,
  "_sha256": "cc10832e2910323345e018240878404fcf073f6c23456bade1c09bedaf83d322",
  "_expires": "2027-01-28T19:48:12.000Z",
  "_created": "2026-10-20T19:39:30.000Z",
  "_published": "2026-10-20T19:48:14.671Z",
  "_buildurl": "https://github.com/r-universe/ajbass/actions/runs/39484445257",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 118844320856,
      "time": 184,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12292764019"
    },
    {
      "job": 118844321009,
      "time": 188,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12293292098"
    },
    {
      "job": 118844320895,
      "time": 184,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12293920788"
    },
    {
      "job": 118844320800,
      "time": 175,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12292554807"
    },
    {
      "job": 118844320795,
      "time": 126,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12294000648"
    },
    {
      "job": 118844321086,
      "time": 304,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12294015958"
    },
    {
      "job": 118844320896,
      "time": 123,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12294305404"
    },
    {
      "job": 118844320870,
      "time": 386,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12293118434"
    },
    {
      "job": 118841265010,
      "time": 375,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12292868270"
    },
    {
      "job": 118844320874,
      "time": 127,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12292943643"
    },
    {
      "job": 118844321026,
      "time": 284,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12293332719"
    },
    {
      "job": 118844321027,
      "time": 155,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12292928549"
    },
    {
      "job": 118844321322,
      "time": 187,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12292893072"
    },
    {
      "job": 118844321279,
      "time": 240,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12292634995"
    },
    {
      "job": 118844320965,
      "time": 171,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12292464841"
    }
  ],
  "_upstream": "https://github.com/ajbass/sffdr",
  "_commit": {
    "id": "0153e7017651b06798bf01f40087ebfe4a04c219",
    "author": "Andrew Bass <ajb359@gmail.com>",
    "committer": "Andrew Bass <ajb359@gmail.com>",
    "message": "README: drop the perfect-LD note and the monotonicity section\n",
    "time": 1792521947
  },
  "_maintainer": {
    "name": "Andrew Bass",
    "email": "ab3105@cam.ac.uk",
    "login": "ajbass",
    "description": "Researcher, PhD @StoreyLab ",
    "uuid": 7573657
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "locfit",
      "role": "Imports"
    },
    {
      "package": "splines",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.5.1",
      "role": "Imports"
    },
    {
      "package": "patchwork",
      "version": ">= 1.3.0",
      "role": "Imports"
    },
    {
      "package": "qvalue",
      "role": "Imports"
    },
    {
      "package": "fastglm",
      "role": "Imports"
    },
    {
      "package": "withr",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "ajbass",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-07",
      "n": 18
    },
    {
      "week": "2026-08",
      "n": 1
    },
    {
      "week": "2026-09",
      "n": 20
    },
    {
      "week": "2026-10",
      "n": 3
    },
    {
      "week": "2026-13",
      "n": 1
    },
    {
      "week": "2026-14",
      "n": 3
    },
    {
      "week": "2026-42",
      "n": 2
    },
    {
      "week": "2026-43",
      "n": 2
    }
  ],
  "_tags": [
    {
      "name": "v1.1.0",
      "date": "2026-02-12"
    },
    {
      "name": "v1.1.2",
      "date": "2026-03-31"
    },
    {
      "name": "v1.1.3",
      "date": "2026-10-17"
    },
    {
      "name": "v1.1.4",
      "date": "2026-10-19"
    }
  ],
  "_stars": 5,
  "_contributors": [
    {
      "user": "ajbass",
      "count": 51,
      "uuid": 7573657
    }
  ],
  "_userbio": {
    "uuid": 7573657,
    "type": "user",
    "name": "Andrew Bass",
    "followers": 33,
    "description": "Researcher, PhD @StoreyLab "
  },
  "_downloads": {
    "count": 270,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/sffdr"
  },
  "_devurl": "https://github.com/ajbass/sffdr",
  "_searchresults": 36,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "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",
    "extra/sffdr.html",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/ajbass/sffdr",
  "_realowner": "ajbass",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2024-12-02"
    },
    {
      "version": "1.1.0",
      "date": "2026-02-16"
    },
    {
      "version": "1.1.2",
      "date": "2026-03-31"
    }
  ],
  "_exports": [
    "decorrelate_informative",
    "discover_empirical_nulls",
    "estimate_overlap",
    "estimate_rho_overlap",
    "fpi0est",
    "fpvalues",
    "kernelEstimator",
    "monoSmooth_conditional",
    "monoSmooth_pava",
    "overlap_null_density",
    "pi0_model",
    "run_empirical_overlap_correction",
    "sffdr"
  ],
  "_datasets": [
    {
      "name": "sumstats",
      "title": "Subset of p-values from the UK Biobank",
      "object": "bmi",
      "class": [
        "data.frame"
      ],
      "fields": [
        "bmi",
        "bfp",
        "cholesterol",
        "triglycerides"
      ],
      "rows": 10000,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "bmi",
      "title": "Subset of p-values from the UK Biobank",
      "topics": [
        "bmi",
        "sumstats"
      ]
    },
    {
      "page": "decorrelate_informative",
      "title": "Decorrelate the informative studies from the primary study",
      "topics": [
        "decorrelate_informative"
      ]
    },
    {
      "page": "estimate_overlap",
      "title": "Estimate the overlap correlation between studies",
      "topics": [
        "estimate_overlap"
      ]
    },
    {
      "page": "fpi0est",
      "title": "Estimate Functional Proportion of Null Tests",
      "topics": [
        "fpi0est"
      ]
    },
    {
      "page": "fpvalues",
      "title": "Functional p-values",
      "topics": [
        "fpvalues"
      ]
    },
    {
      "page": "kernelEstimator",
      "title": "Kernel Density Estimation for GWAS P-values",
      "topics": [
        "kernelEstimator"
      ]
    },
    {
      "page": "monoSmooth_conditional",
      "title": "Fast Conditional Monotonic Smoothing",
      "topics": [
        "monoSmooth_conditional"
      ]
    },
    {
      "page": "monoSmooth_pava",
      "title": "Fast Conditional PAVA (Decreasing)",
      "topics": [
        "monoSmooth_pava"
      ]
    },
    {
      "page": "pi0_model",
      "title": "Build Model for Functional Proportion of Null Tests (fpi0)",
      "topics": [
        "pi0_model"
      ]
    },
    {
      "page": "plot.sffdr",
      "title": "Plotting function for sffdr object",
      "topics": [
        "plot,",
        "plot.sffdr"
      ]
    },
    {
      "page": "sffdr",
      "title": "Surrogate Functional False Discovery Rate Analysis",
      "topics": [
        "sffdr"
      ]
    }
  ],
  "_readme": "https://github.com/ajbass/sffdr/raw/HEAD/README.md",
  "_rundeps": [
    "BH",
    "bigmemory",
    "bigmemory.sri",
    "cli",
    "cpp11",
    "farver",
    "fastglm",
    "Formula",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "locfit",
    "magrittr",
    "Matrix",
    "patchwork",
    "plyr",
    "qvalue",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "reshape2",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "uuid",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "sffdr.Rmd",
      "filename": "sffdr.html",
      "title": "sffdr Package Vignette",
      "author": "Andrew J. Bass and Chris Wallace",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Citing this package",
        "Getting help",
        "Installation",
        "Quick start guide",
        "1. Modeling the functional proportion of null tests $\\pi_{0}(z)$",
        "2. Estimating the functional significance quantities",
        "3. Incorporating linkage disequilibrium (LD)",
        "Advanced usage",
        "Enforcing monotonicity",
        "Incorporating LD scores",
        "Sample overlap with the informative studies",
        "Manual Knot Selection and using other informative variables"
      ],
      "created": "2024-09-18 08:06:19",
      "modified": "2026-10-19 19:13:55",
      "commits": 21
    }
  ],
  "_score": 5.857332496431268,
  "_indexed": true,
  "_nocasepkg": "sffdr",
  "_universes": [
    "ajbass"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.4",
      "date": "2026-10-20T19:42:14.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "0153e7017651b06798bf01f40087ebfe4a04c219",
      "fileid": "https://r2.ropensci.org/384d2f22e812a4b80102c99f1115700df8de670590dd97f62a4f25e6fb7d6dc3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ajbass/actions/runs/39484445257"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.4",
      "date": "2026-10-20T19:42:07.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "0153e7017651b06798bf01f40087ebfe4a04c219",
      "fileid": "https://r2.ropensci.org/54e045d66bd460840c9f58ed15d6d0c5a650c5ae7162f53e9a74ae02e546d62b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ajbass/actions/runs/39484445257"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.1.4",
      "date": "2026-10-20T19:42:15.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "0153e7017651b06798bf01f40087ebfe4a04c219",
      "fileid": "https://r2.ropensci.org/2585793a10cbdeef992b61969b477ba5078178ce956dea217d7f0946501ae78d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ajbass/actions/runs/39484445257"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.1.4",
      "date": "2026-10-20T19:42:06.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "0153e7017651b06798bf01f40087ebfe4a04c219",
      "fileid": "https://r2.ropensci.org/40985224c152812d23eff14b8d21345bd05180fa51e1e31908ef98f200e7d87b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ajbass/actions/runs/39484445257"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.4",
      "date": "2026-10-20T19:43:07.000Z",
      "arch": "aarch64",
      "commit": "0153e7017651b06798bf01f40087ebfe4a04c219",
      "fileid": "https://r2.ropensci.org/4b4fce830367dd69f0dcfcd82249d902ce4dd7ce3ea5b73970932fbdcbd69429",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ajbass/actions/runs/39484445257"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.4",
      "date": "2026-10-20T19:44:11.000Z",
      "arch": "x86_64",
      "commit": "0153e7017651b06798bf01f40087ebfe4a04c219",
      "fileid": "https://r2.ropensci.org/258fa6d21e4314bfe490716b2741e7d6bf215f78c9471897dcbf97c34d8d67de",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ajbass/actions/runs/39484445257"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.1.4",
      "date": "2026-10-20T19:45:17.000Z",
      "arch": "aarch64",
      "commit": "0153e7017651b06798bf01f40087ebfe4a04c219",
      "fileid": "https://r2.ropensci.org/ad2d7e4adc1aec20cc0c118e175292f2041b31b8172292179f2f58877f570993",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ajbass/actions/runs/39484445257"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.1.4",
      "date": "2026-10-20T19:45:07.000Z",
      "arch": "x86_64",
      "commit": "0153e7017651b06798bf01f40087ebfe4a04c219",
      "fileid": "https://r2.ropensci.org/ffdec1761a3a88ee5ec07417f379ac87ae984d5afce05ecf9105dd22d7e2c05a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ajbass/actions/runs/39484445257"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.4",
      "date": "2026-10-20T19:41:57.000Z",
      "arch": "emscripten",
      "commit": "0153e7017651b06798bf01f40087ebfe4a04c219",
      "fileid": "https://r2.ropensci.org/c6f3dda4bd6e026cb680169b806cf1e02cf2a83aebe3919aac8a93f09657effd",
      "status": "success",
      "buildurl": "https://github.com/r-universe/ajbass/actions/runs/39484445257"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.4",
      "date": "2026-10-20T19:43:32.000Z",
      "arch": "aarch64",
      "commit": "0153e7017651b06798bf01f40087ebfe4a04c219",
      "fileid": "https://r2.ropensci.org/2f21c762b4c7a07663af32b183d7cb465360932a1146c87961d58ac91c5c18be",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ajbass/actions/runs/39484445257"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.4",
      "date": "2026-10-20T19:40:49.000Z",
      "arch": "x86_64",
      "commit": "0153e7017651b06798bf01f40087ebfe4a04c219",
      "fileid": "https://r2.ropensci.org/92e1fc67fafc224f081d3d9c8095320bd0d65210917530344b00e67e539a1063",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ajbass/actions/runs/39484445257"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.4",
      "date": "2026-10-20T19:41:07.000Z",
      "arch": "x86_64",
      "commit": "0153e7017651b06798bf01f40087ebfe4a04c219",
      "fileid": "https://r2.ropensci.org/e70322871b36e2751a5755fac7af1385c99028e7e8730b9408c988134e988d4e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ajbass/actions/runs/39484445257"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.1.4",
      "date": "2026-10-20T19:42:53.000Z",
      "arch": "aarch64",
      "commit": "0153e7017651b06798bf01f40087ebfe4a04c219",
      "fileid": "https://r2.ropensci.org/d9514d50f6b2f4832e7e6e98ff589a0fce236bf72817223fa75995e8df1bf3e2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ajbass/actions/runs/39484445257"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.1.4",
      "date": "2026-10-20T19:41:17.000Z",
      "arch": "x86_64",
      "commit": "0153e7017651b06798bf01f40087ebfe4a04c219",
      "fileid": "https://r2.ropensci.org/ea0f296511ff2a6a6d65c94f52e91d2839addd0c4f474117afc2ca2eac64573b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ajbass/actions/runs/39484445257"
    }
  ]
}