{
  "_id": "6ac7ba2cde46216d5edd2bf1",
  "Package": "MRAPSS",
  "Title": "Mendelian Randomization Accounting for Pleiotropy and Sample\nStructure",
  "Version": "0.0.0.9000",
  "Authors@R": "person(given = \"Xianghong\",\nfamily = \"HU\",\nrole = c(\"aut\", \"cre\"),\nemail = \"maxhu@ust.hk\",\ncomment = c(ORCID = \"0000-0001-5260-3936\"))",
  "Description": "Implements the MR-APSS approach to test for the causal\neffects between an exposure and an outcome disease. MR-APSS is\na unified approach to Mendelian Randomization accounting for\npolygenicity, pleiotropy and sample structure using genome-wide\nsummary statistics. Specifically, MR-APSS uses a\nbackground-foreground model to characterize both SNP-exposure\neffects and SNP-outcome effects estimates, where the background\nmodel accounts for confounding from genetic correlation and\nsample structure and the foreground model captures the valid\nsignal for causal inference.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "LazyDataCompression": "xz",
  "Remotes": [
    "mrcieu/ieugwasr"
  ],
  "Config/roxygen2/version": "8.1.0",
  "Config/pak/sysreqs": "libssl-dev libx11-dev",
  "Repository": "https://mrcieu.r-universe.dev",
  "Date/Publication": "2026-08-11 13:12:52 UTC",
  "RemoteUrl": "https://github.com/remlapmot/MR-APSS",
  "RemoteRef": "suggestions",
  "RemoteSha": "ac1e457511b91c8a0b555a048dfd963633ac89a9",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-08 15:38:14 UTC",
    "User": "root"
  },
  "Author": "Xianghong HU [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-5260-3936>)",
  "Maintainer": "Xianghong HU <maxhu@ust.hk>",
  "_user": "mrcieu",
  "_type": "src",
  "_file": "MRAPSS_0.0.0.9000.tar.gz",
  "_fileid": "https://r2.ropensci.org/2c435f7175113b53991215a24405cb7168d050f71a98e4a5bb886b8a75627b51",
  "_filesize": 5161398,
  "_sha256": "2c435f7175113b53991215a24405cb7168d050f71a98e4a5bb886b8a75627b51",
  "_expires": "2027-01-16T15:43:35.000Z",
  "_created": "2026-10-08T15:38:14.000Z",
  "_published": "2026-10-08T15:43:40.214Z",
  "_buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37801890426",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 113398069539,
      "time": 242,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11561748287"
    },
    {
      "job": 113398069714,
      "time": 238,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11561358400"
    },
    {
      "job": 113398069414,
      "time": 247,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11561377674"
    },
    {
      "job": 113398069485,
      "time": 196,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11560593739"
    },
    {
      "job": 113396126856,
      "time": 242,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11560414434"
    },
    {
      "job": 113398069351,
      "time": 140,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11561558131"
    },
    {
      "job": 113398069574,
      "time": 188,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11560778263"
    },
    {
      "job": 113398069649,
      "time": 221,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11561248244"
    },
    {
      "job": 113398069461,
      "time": 191,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11560803606"
    }
  ],
  "_upstream": "https://github.com/remlapmot/MR-APSS",
  "_commit": {
    "id": "ac1e457511b91c8a0b555a048dfd963633ac89a9",
    "author": "Tom Palmer <remlapmot@hotmail.com>",
    "committer": "Tom Palmer <remlapmot@hotmail.com>",
    "message": "Document\n",
    "time": 1786453972
  },
  "_maintainer": {
    "name": "Xianghong HU",
    "email": "maxhu@ust.hk",
    "login": "hxh0504",
    "description": "",
    "uuid": 64360832,
    "orcid": "0000-0001-5260-3936"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "ieugwasr",
      "version": ">= 0.1.4",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "expm",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "mvtnorm",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "remlapmot",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-18",
      "n": 1
    },
    {
      "week": "2026-33",
      "n": 5
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "hxh0928",
      "count": 18,
      "uuid": 137586273
    }
  ],
  "_userbio": {
    "uuid": 15654827,
    "type": "organization",
    "name": "MRC Integrative Epidemiology Unit",
    "followers": 257
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/MRAPSS"
  },
  "_devurl": "https://github.com/remlapmot/mr-apss",
  "_searchresults": 35,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/MRAPSS.html",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_cranurl": false,
  "_exports": [
    "clump",
    "est_paras",
    "format_data",
    "MR_EM_fix_rf_func",
    "MR_fix_rf",
    "MRAPSS",
    "MRplot",
    "sensitivity"
  ],
  "_datasets": [
    {
      "name": "C",
      "title": "Estimated C matrix for the BMI-T2D example",
      "object": "C",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "V1",
        "V2"
      ],
      "rows": 2,
      "table": true,
      "tojson": true
    },
    {
      "name": "MHC.SNPs",
      "title": "SNPs in the MHC region",
      "object": "MHC.SNPs",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "MRdat",
      "title": "Harmonized instrument data for the BMI-T2D example",
      "object": "MRdat",
      "class": [
        "data.frame"
      ],
      "fields": [
        "SNP",
        "A1",
        "A2",
        "b.exp",
        "b.out",
        "se.exp",
        "se.out",
        "pval.exp",
        "pval.out",
        "L2",
        "Threshold"
      ],
      "rows": 1227,
      "table": true,
      "tojson": true
    },
    {
      "name": "Omega",
      "title": "Estimated Omega matrix for the BMI-T2D example",
      "object": "Omega",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "V1",
        "V2"
      ],
      "rows": 2,
      "table": true,
      "tojson": true
    },
    {
      "name": "w_hm3.snplist",
      "title": "HapMap 3 SNP list",
      "object": "w_hm3.snplist",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "SNP",
        "A1",
        "A2"
      ],
      "rows": 1217311,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "C",
      "title": "Estimated C matrix for the BMI-T2D example",
      "topics": [
        "C"
      ]
    },
    {
      "page": "clump",
      "title": "Perform LD clumping",
      "topics": [
        "clump"
      ]
    },
    {
      "page": "est_paras",
      "title": "A function harmonizing datasets and estimate background parameters by LD score regression.",
      "topics": [
        "est_paras"
      ]
    },
    {
      "page": "format_data",
      "title": "Format GWAS summary data for MR-APSS.",
      "topics": [
        "format_data"
      ]
    },
    {
      "page": "MHC.SNPs",
      "title": "SNPs in the MHC region",
      "topics": [
        "MHC.SNPs"
      ]
    },
    {
      "page": "MR_EM_fix_rf_func",
      "title": "Variational EM algorithm for MR-APSS with a correlated foreground model.",
      "topics": [
        "MR_EM_fix_rf_func"
      ]
    },
    {
      "page": "MR_fix_rf",
      "title": "A function for causal effect estimation and inference in sensitivity analysis.",
      "topics": [
        "MR_fix_rf"
      ]
    },
    {
      "page": "MRAPSS",
      "title": "A function for implementing MR-APSS.",
      "topics": [
        "MRAPSS"
      ]
    },
    {
      "page": "MRdat",
      "title": "Harmonized instrument data for the BMI-T2D example",
      "topics": [
        "MRdat"
      ]
    },
    {
      "page": "MRplot",
      "title": "Visualize the MR-APSS analysis results",
      "topics": [
        "MRplot"
      ]
    },
    {
      "page": "Omega",
      "title": "Estimated Omega matrix for the BMI-T2D example",
      "topics": [
        "Omega"
      ]
    },
    {
      "page": "sensitivity",
      "title": "Sensitivity analysis for the foreground correlation parameter r.",
      "topics": [
        "sensitivity"
      ]
    },
    {
      "page": "w_hm3.snplist",
      "title": "HapMap 3 SNP list",
      "topics": [
        "w_hm3.snplist"
      ]
    }
  ],
  "_readme": "https://github.com/remlapmot/MR-APSS/raw/suggestions/README.md",
  "_rundeps": [
    "askpass",
    "bit",
    "bit64",
    "cli",
    "clipr",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "dplyr",
    "expm",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "hms",
    "httr",
    "ieugwasr",
    "isoband",
    "jsonlite",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "mime",
    "mvtnorm",
    "openssl",
    "pillar",
    "pkgconfig",
    "prettyunits",
    "progress",
    "R6",
    "RColorBrewer",
    "readr",
    "rlang",
    "S7",
    "scales",
    "sys",
    "tibble",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr"
  ],
  "_score": 2.5440680443502757,
  "_indexed": false,
  "_nocasepkg": "mrapss",
  "_universes": [
    "mrcieu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.0.0.9000",
      "date": "2026-10-08T15:40:57.000Z",
      "distro": "resolute",
      "commit": "ac1e457511b91c8a0b555a048dfd963633ac89a9",
      "fileid": "https://r2.ropensci.org/f681fbf53a4ed845f5450eee834df0caa7dc074e4424017f63d801cff2ebc7ff",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37801890426"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.0.0.9000",
      "date": "2026-10-08T15:40:53.000Z",
      "distro": "resolute",
      "commit": "ac1e457511b91c8a0b555a048dfd963633ac89a9",
      "fileid": "https://r2.ropensci.org/67e4aefaee4b3cdd374c68be614ee9081e3fd7e46b1f4e41d8efe4c3e93be551",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37801890426"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.0.0.9000",
      "date": "2026-10-08T15:41:01.000Z",
      "commit": "ac1e457511b91c8a0b555a048dfd963633ac89a9",
      "fileid": "https://r2.ropensci.org/0350234591e694b732c72cf17d923d073053c4d6b0d018508a43ed7e444317fc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37801890426"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.0.0.9000",
      "date": "2026-10-08T15:40:27.000Z",
      "commit": "ac1e457511b91c8a0b555a048dfd963633ac89a9",
      "fileid": "https://r2.ropensci.org/1a5b28aaddfa0a9f787c4dcad4f5cc2b2534332c2f005241fb92adef07456da5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37801890426"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.0.0.9000",
      "date": "2026-10-08T15:41:00.000Z",
      "commit": "ac1e457511b91c8a0b555a048dfd963633ac89a9",
      "fileid": "https://r2.ropensci.org/e75169f3b207651db9dba741255461e0b13c6e411191066425f35c95e1c8be29",
      "status": "success",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37801890426"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.0.0.9000",
      "date": "2026-10-08T15:39:56.000Z",
      "commit": "ac1e457511b91c8a0b555a048dfd963633ac89a9",
      "fileid": "https://r2.ropensci.org/b12b90f20b5814fc98445fdd3d9943ed046398c639d091c1b46331bc8b09f95e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37801890426"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.0.0.9000",
      "date": "2026-10-08T15:39:58.000Z",
      "commit": "ac1e457511b91c8a0b555a048dfd963633ac89a9",
      "fileid": "https://r2.ropensci.org/5a82aa07bb080544843bfff5822f0ab3681d52177107234e929942343a87fc17",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37801890426"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.0.0.9000",
      "date": "2026-10-08T15:39:52.000Z",
      "commit": "ac1e457511b91c8a0b555a048dfd963633ac89a9",
      "fileid": "https://r2.ropensci.org/7a79ccefdeed236922ab86f4fbbe408ee66324e3a29e83f43dbc027e9d3eeb04",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37801890426"
    }
  ]
}