{
  "_id": "6a1d6b621d7bb097a0a4f5cb",
  "Package": "CoxMK",
  "Type": "Package",
  "Title": "A Model-X Knockoff Method for Genome-Wide Survival Association\nAnalysis",
  "Version": "0.1.1",
  "Author": "Yang Chen [aut, cre], Contributors [ctb]",
  "Maintainer": "Yang Chen <yangchen5@stu.scu.edu.cn>",
  "Authors@R": "c(\nperson(\"Yang\", \"Chen\", email = \"yangchen5@stu.scu.edu.cn\", role = c(\"aut\", \"cre\")),\nperson(\"Contributors\", \"\", role = \"ctb\")\n)",
  "Description": "A genome-wide survival framework that integrates\nsequential conditional independent tuples and saddlepoint\napproximation method, to provide SNP-level false discovery rate\ncontrol while improving power, particularly for biobank-scale\nsurvival analyses with low event rates. The method is based on\nmodel-X knockoffs as described in Barber and Candes (2015)\n<doi:10.1214/15-AOS1337> and fast survival analysis methods\nfrom Bi et al. (2020) <doi:10.1016/j.ajhg.2020.06.003>. A\nshrinkage algorithmic leveraging accelerates multiple knockoffs\ngeneration in large genetic cohorts. This CRAN version uses\nstandard Cox regression for association testing. For enhanced\nperformance on very large datasets, users may optionally\ninstall the 'SPACox' package from GitHub which provides\nsaddlepoint approximation methods for survival analysis.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "Config/testthat/edition": "3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-01 11:18:35 UTC",
    "User": "root"
  },
  "Repository": "https://xiaoxiandadada.r-universe.dev",
  "Date/Publication": "2025-09-03 08:40:26 UTC",
  "RemoteUrl": "https://github.com/cran/CoxMK",
  "RemoteRef": "HEAD",
  "RemoteSha": "d67167c12b5c469419e443f34ea41e3efa9e2cfe",
  "MD5sum": "dd5fce2c1b7a11e17e00573a135b684f",
  "_user": "xiaoxiandadada",
  "_type": "src",
  "_file": "CoxMK_0.1.1.tar.gz",
  "_fileid": "c327af8066b6cd466e5f9b40e253aa8b5e9095254eff83f9aa58742021a943e1",
  "_filesize": 171133,
  "_sha256": "c327af8066b6cd466e5f9b40e253aa8b5e9095254eff83f9aa58742021a943e1",
  "_created": "2026-06-01T11:18:35.000Z",
  "_published": "2026-06-01T11:22:10.158Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78840971596,
      "time": 133,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7330111873"
    },
    {
      "job": 78840971632,
      "time": 110,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7330104066"
    },
    {
      "job": 78840971584,
      "time": 171,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7330113614"
    },
    {
      "job": 78840971509,
      "time": 179,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7330112572"
    },
    {
      "job": 78840589762,
      "time": 146,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7330069440"
    },
    {
      "job": 78840971580,
      "time": 93,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7330099054"
    },
    {
      "job": 78840971572,
      "time": 105,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7330102369"
    },
    {
      "job": 78840971579,
      "time": 92,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7330097999"
    },
    {
      "job": 78840971512,
      "time": 98,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7330099748"
    }
  ],
  "_buildurl": "https://github.com/r-universe/xiaoxiandadada/actions/runs/26751545473",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/CoxMK",
  "_commit": {
    "id": "d67167c12b5c469419e443f34ea41e3efa9e2cfe",
    "author": "Yang Chen <yangchen5@stu.scu.edu.cn>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.1.1\n",
    "time": 1756888826
  },
  "_maintainer": {
    "name": "Yang Chen",
    "email": "yangchen5@stu.scu.edu.cn",
    "login": "xiaoxiandadada",
    "description": "",
    "uuid": 92154745
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "survival",
      "role": "Imports"
    },
    {
      "package": "irlba",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "gdsfmt",
      "role": "Imports"
    },
    {
      "package": "BEDMatrix",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-36",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "0.1.1",
      "date": "2025-09-03"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "xiaoxiandadada",
      "count": 1,
      "uuid": 92154745
    }
  ],
  "_userbio": {
    "uuid": 92154745,
    "type": "user",
    "name": "Chen Yang"
  },
  "_downloads": {
    "count": 143,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/CoxMK"
  },
  "_searchresults": 6,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/CoxMK.html",
    "manual.pdf"
  ],
  "_realowner": "xiaoxiandadada",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1.1",
      "date": "2025-09-03"
    }
  ],
  "_exports": [
    "calculate_w_statistics",
    "cox_knockoff_analysis",
    "create_knockoffs",
    "fit_cox_model_from_files",
    "fit_null_cox_model",
    "knockoff_filter",
    "perform_association_testing"
  ],
  "_help": [
    {
      "page": "calculate_w_statistics",
      "title": "Calculate W Statistics for Knockoff Analysis",
      "topics": [
        "calculate_w_statistics"
      ]
    },
    {
      "page": "cox_knockoff_analysis",
      "title": "Complete Cox Knockoff Analysis Workflow",
      "topics": [
        "cox_knockoff_analysis"
      ]
    },
    {
      "page": "CoxMK",
      "title": "CoxMK: Cox Regression with Multiple Knockoffs",
      "topics": [
        "CoxMK"
      ]
    },
    {
      "page": "create_knockoffs",
      "title": "Create Multiple Knockoffs for Genetic Data",
      "topics": [
        "create_knockoffs"
      ]
    },
    {
      "page": "fit_cox_model_from_files",
      "title": "Step 2: Fit Cox Model from Files",
      "topics": [
        "fit_cox_model_from_files"
      ]
    },
    {
      "page": "fit_null_cox_model",
      "title": "Fit Null Cox Model",
      "topics": [
        "fit_null_cox_model"
      ]
    },
    {
      "page": "knockoff_filter",
      "title": "Apply Knockoff Filter for Variable Selection",
      "topics": [
        "knockoff_filter"
      ]
    },
    {
      "page": "load_knockoff_gds",
      "title": "Load Knockoff Data from GDS File",
      "topics": [
        "load_knockoff_gds"
      ]
    },
    {
      "page": "perform_association_testing",
      "title": "Perform Association Testing",
      "topics": [
        "perform_association_testing"
      ]
    }
  ],
  "_rundeps": [
    "BEDMatrix",
    "crochet",
    "gdsfmt",
    "irlba",
    "lattice",
    "Matrix",
    "survival"
  ],
  "_score": 1,
  "_indexed": true,
  "_nocasepkg": "coxmk",
  "_universes": [
    "xiaoxiandadada"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-06-01T11:20:38.000Z",
      "distro": "noble",
      "commit": "d67167c12b5c469419e443f34ea41e3efa9e2cfe",
      "fileid": "cd79c195847f0e3a026cc6e6dd434e7e23fca7b9a2004b2828c391f2878fddbb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/xiaoxiandadada/actions/runs/26751545473"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-06-01T11:20:18.000Z",
      "distro": "noble",
      "commit": "d67167c12b5c469419e443f34ea41e3efa9e2cfe",
      "fileid": "8816ca71d97ab4d5a23cbbd0c178c9cab8c686ffdfafb40e7d7beeff37b36034",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/xiaoxiandadada/actions/runs/26751545473"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-06-01T11:20:54.000Z",
      "commit": "d67167c12b5c469419e443f34ea41e3efa9e2cfe",
      "fileid": "142f19d1bffcde664e62170071e0aac9ab9dc7a4b89017cb9f7cacffce3362ba",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/xiaoxiandadada/actions/runs/26751545473"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-06-01T11:20:48.000Z",
      "commit": "d67167c12b5c469419e443f34ea41e3efa9e2cfe",
      "fileid": "63daa3f4d63bbbaa2b823271e4ac7ee16429c7d722485bb0837810814f360e3d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/xiaoxiandadada/actions/runs/26751545473"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.1",
      "date": "2026-06-01T11:20:28.000Z",
      "commit": "d67167c12b5c469419e443f34ea41e3efa9e2cfe",
      "fileid": "9d347b739affd0699281e09d5e7ac231c1a7df33f6cb4c9a2c31d2ef240dfcb9",
      "status": "success",
      "buildurl": "https://github.com/r-universe/xiaoxiandadada/actions/runs/26751545473"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-06-01T11:20:13.000Z",
      "commit": "d67167c12b5c469419e443f34ea41e3efa9e2cfe",
      "fileid": "10876f4b83db202f1d8c12dac6d0fe1c1f92aab3ed388888c4295de5bd5ebcfe",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/xiaoxiandadada/actions/runs/26751545473"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-06-01T11:19:49.000Z",
      "commit": "d67167c12b5c469419e443f34ea41e3efa9e2cfe",
      "fileid": "36cc0abeac514a0381d6a2c65112b1f25522ead05ca0b2f4558fbdde4df1efc3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/xiaoxiandadada/actions/runs/26751545473"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-06-01T11:19:49.000Z",
      "commit": "d67167c12b5c469419e443f34ea41e3efa9e2cfe",
      "fileid": "022e3b645039cecb2aff931069e9042590b2a431622ded50373ba9fc14c2d9c1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/xiaoxiandadada/actions/runs/26751545473"
    }
  ]
}