{
  "_id": "6ab5d34cc18b73ce90b50d09",
  "Package": "integIRTy",
  "Type": "Package",
  "LazyData": "true",
  "Title": "Integrating Multiple Modalities of High Throughput Assays Using\nItem Response Theory",
  "Version": "1.0.9",
  "Date": "2026-09-24",
  "Authors@R": "c(person(given = \"Pan\", family = \"Tong\", role = \"aut\"),\nperson(given = c(\"Kevin\", \"R.\"), family = \"Coombes\",\nrole = c(\"aut\", \"cre\"), email = \"krc@silicovore.com\"))",
  "Description": "Provides a systematic framework for integrating multiple\nmodalities of assays profiled on the same set of samples. The\ngoal is to identify genes that are altered in cancer either\nmarginally or consistently across different assays. The\nheterogeneity among different platforms and different samples\nare automatically adjusted so that the overall alteration\nmagnitude can be accurately inferred. See Tong and Coombes\n(2012) <doi:10.1093/bioinformatics/bts561>.",
  "License": "Apache License (== 2.0)",
  "URL": "http://silicovore.com/OOMPA/standalone.html",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-25 01:46:46 UTC",
    "User": "root"
  },
  "Author": "Pan Tong [aut], Kevin R. Coombes [aut, cre]",
  "Maintainer": "Kevin R. Coombes <krc@silicovore.com>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-09-24 21:50:02 UTC",
  "RemoteUrl": "https://github.com/cran/integIRTy",
  "RemoteRef": "HEAD",
  "RemoteSha": "1fc9f46b145b6b50188ec00f743f62906aa51670",
  "_user": "cran",
  "_type": "src",
  "_file": "integIRTy_1.0.9.tar.gz",
  "_fileid": "https://r2.ropensci.org/68f76289d830030c1e35593ae942be00ad08a21a36dc9982c56cddfe58f5e56f",
  "_filesize": 1361234,
  "_sha256": "68f76289d830030c1e35593ae942be00ad08a21a36dc9982c56cddfe58f5e56f",
  "_expires": "2027-01-03T01:50:01.000Z",
  "_created": "2026-09-25T01:46:46.000Z",
  "_published": "2026-09-25T01:50:04.111Z",
  "_jobs": [
    {
      "job": 107910298162,
      "time": 143,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10842482574"
    },
    {
      "job": 107910298107,
      "time": 154,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10842517442"
    },
    {
      "job": 107909543660,
      "time": 213,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10842902689"
    },
    {
      "job": 107910298079,
      "time": 124,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10843400649"
    },
    {
      "job": 107910298086,
      "time": 92,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10842467459"
    },
    {
      "job": 107910298254,
      "time": 90,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10842602201"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/36083222998",
  "_status": "success",
  "_upstream": "https://github.com/cran/integIRTy",
  "_commit": {
    "id": "1fc9f46b145b6b50188ec00f743f62906aa51670",
    "author": "Kevin R. Coombes <krc@silicovore.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.0.9\n",
    "time": 1790286602
  },
  "_maintainer": {
    "name": "Kevin R. Coombes",
    "email": "krc@silicovore.com"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "ltm",
      "role": "Depends"
    },
    {
      "package": "foreach",
      "role": "Depends"
    },
    {
      "package": "doParallel",
      "role": "Depends"
    },
    {
      "package": "mclust",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "abind",
      "role": "Imports"
    },
    {
      "package": "KernSmooth",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-39",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "1.0.9",
      "date": "2026-09-24"
    }
  ],
  "_stars": 0,
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "followers": 630,
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 344,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/integIRTy"
  },
  "_searchresults": 27,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/integIRTy.html",
    "extra/manual.pdf"
  ],
  "_realowner": "cran",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.5",
      "date": "2017-07-11"
    },
    {
      "version": "1.0.6",
      "date": "2019-05-06"
    },
    {
      "version": "1.0.7",
      "date": "2022-05-03"
    },
    {
      "version": "1.0.8",
      "date": "2025-04-08"
    }
  ],
  "_exports": [
    "calculatePermutedScoreByGeneSampling",
    "computeAbility",
    "dichotomize",
    "dichotomizeCN",
    "dichotomizeExpr",
    "dichotomizeMethy",
    "fitOnSinglePlat",
    "intIRTeasyRun",
    "intIRTeasyRunFromRaw",
    "simulateBinaryResponseMat"
  ],
  "_datasets": [
    {
      "name": "CN_N",
      "title": "Ovarian Cancer Datasets",
      "object": "OV",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "TCGA-13-0720-10B-01D-0508-04",
        "TCGA-13-0797-10A-01D-0508-04",
        "TCGA-13-0717-10B-01D-0508-04",
        "TCGA-13-0765-10A-01D-0508-04",
        "TCGA-13-0757-10A-01D-0508-04",
        "TCGA-13-0768-10A-01D-0508-04",
        "TCGA-13-0764-10A-01D-0508-04",
        "TCGA-13-0795-10A-01D-0508-04",
        "TCGA-13-0805-10A-01D-0508-04",
        "TCGA-09-0364-10A-01D-0508-04",
        "TCGA-13-0724-10B-01D-0508-04",
        "TCGA-13-0714-10B-01D-0508-04",
        "TCGA-13-0800-10A-01D-0508-04",
        "TCGA-13-0755-10A-01D-0508-04",
        "TCGA-13-0766-10A-01D-0508-04",
        "TCGA-13-0799-10A-01D-0508-04",
        "TCGA-09-0369-10C-01D-0508-04",
        "TCGA-13-0727-10B-01D-0508-04",
        "TCGA-13-0762-10A-01D-0508-04",
        "TCGA-13-0794-10A-01D-0508-04",
        "TCGA-13-0804-10A-01D-0508-04",
        "TCGA-13-0758-10A-01D-0508-04",
        "TCGA-13-0791-10A-01D-0508-04",
        "TCGA-13-0801-10A-01D-0508-04",
        "TCGA-09-0367-10A-01D-0508-04",
        "TCGA-13-0726-10B-01D-0508-04",
        "TCGA-13-0761-10A-01D-0508-04",
        "TCGA-13-0793-10A-01D-0508-04",
        "TCGA-13-0792-10A-01D-0508-04",
        "TCGA-13-0802-10A-01D-0508-04"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "CN_T",
      "title": "Ovarian Cancer Datasets",
      "object": "OV",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "TCGA-13-0720-01A-01D-0508-04",
        "TCGA-13-0797-01A-01D-0508-04",
        "TCGA-13-0717-01A-01D-0508-04",
        "TCGA-13-0765-01A-01D-0508-04",
        "TCGA-13-0757-01A-01D-0508-04",
        "TCGA-13-0768-01A-01D-0508-04",
        "TCGA-13-0764-01A-03D-0508-04",
        "TCGA-13-0795-01A-01D-0508-04",
        "TCGA-13-0805-01A-01D-0508-04",
        "TCGA-09-0364-01A-02D-0508-04",
        "TCGA-13-0724-01A-01D-0508-04",
        "TCGA-13-0714-01A-01D-0508-04",
        "TCGA-13-0800-01A-01D-0508-04",
        "TCGA-13-0755-01A-01D-0508-04",
        "TCGA-13-0766-01A-02D-0508-04",
        "TCGA-13-0799-01A-01D-0508-04",
        "TCGA-09-0369-01A-01D-0508-04",
        "TCGA-13-0727-01A-01D-0508-04",
        "TCGA-13-0762-01A-01D-0508-04",
        "TCGA-13-0794-01A-01D-0508-04",
        "TCGA-13-0804-01A-01D-0508-04",
        "TCGA-13-0758-01A-01D-0508-04",
        "TCGA-13-0791-01A-01D-0508-04",
        "TCGA-13-0801-01A-01D-0508-04",
        "TCGA-09-0367-01A-01D-0508-04",
        "TCGA-13-0726-01A-01D-0508-04",
        "TCGA-13-0761-01A-01D-0508-04",
        "TCGA-13-0793-01A-01D-0508-04",
        "TCGA-13-0792-01A-01D-0508-04",
        "TCGA-13-0802-01A-01D-0508-04"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "Expr_N",
      "title": "Ovarian Cancer Datasets",
      "object": "OV",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "TCGA-01-0630-11A-01R-0362-01",
        "TCGA-01-0631-11A-01R-0362-01",
        "TCGA-01-0633-11A-01R-0362-01",
        "TCGA-01-0636-11A-01R-0362-01",
        "TCGA-01-0637-11A-01R-0362-01",
        "TCGA-01-0628-11A-01R-0362-01",
        "TCGA-01-0639-11A-01R-0362-01",
        "TCGA-01-0642-11A-02R-0362-01"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "Expr_T",
      "title": "Ovarian Cancer Datasets",
      "object": "OV",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "TCGA-09-2043-01A-01R-0709-01",
        "TCGA-13-2060-01A-01R-0709-01",
        "TCGA-24-2290-01A-01R-0709-01",
        "TCGA-25-2392-01A-01R-0709-01",
        "TCGA-25-2404-01A-01R-0709-01",
        "TCGA-59-2349-01A-01R-0709-01",
        "TCGA-09-2044-01B-01R-0709-01",
        "TCGA-24-2262-01A-01R-0709-01",
        "TCGA-24-2293-01A-01R-0709-01",
        "TCGA-25-2393-01A-01R-0709-01",
        "TCGA-25-2408-01A-01R-0709-01",
        "TCGA-59-2350-01A-01R-0709-01",
        "TCGA-09-2045-01A-01R-0709-01",
        "TCGA-24-2267-01A-01R-0709-01",
        "TCGA-24-2295-01A-01R-0709-01",
        "TCGA-25-2396-01A-01R-0709-01",
        "TCGA-25-2409-01A-01R-0709-01",
        "TCGA-59-2351-01A-01R-0709-01",
        "TCGA-09-2048-01A-01R-0709-01",
        "TCGA-24-2271-01A-01R-0709-01",
        "TCGA-24-2297-01A-01R-0709-01",
        "TCGA-25-2397-01A-01R-0709-01",
        "TCGA-29-2414-01A-02R-0709-01",
        "TCGA-59-2352-01A-01R-0709-01",
        "TCGA-09-2049-01D-01R-0709-01",
        "TCGA-24-2280-01A-01R-0709-01",
        "TCGA-24-2298-01A-01R-0709-01",
        "TCGA-25-2398-01A-01R-0709-01",
        "TCGA-29-2425-01A-01R-0709-01",
        "TCGA-59-2354-01A-01R-0709-01"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "Methy_N",
      "title": "Ovarian Cancer Datasets",
      "object": "OV",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "TCGA-01-0628-11A-01D-0383-05",
        "TCGA-01-0629-11A-01D-0383-05",
        "TCGA-01-0630-11A-01D-0383-05",
        "TCGA-01-0631-11A-01D-0383-05",
        "TCGA-01-0633-11A-01D-0383-05",
        "TCGA-01-0636-11A-01D-0383-05",
        "TCGA-01-0637-11A-01D-0383-05",
        "TCGA-01-0638-11A-02D-0383-05",
        "TCGA-01-0639-11A-01D-0383-05",
        "TCGA-01-0642-11A-02D-0383-05"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "Methy_T",
      "title": "Ovarian Cancer Datasets",
      "object": "OV",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "TCGA-04-1655-01A-01D-0563-05",
        "TCGA-09-1670-01A-01D-0563-05",
        "TCGA-09-1672-01A-01D-0563-05",
        "TCGA-09-1673-01A-01D-0563-05",
        "TCGA-09-1674-01A-01D-0563-05",
        "TCGA-09-1675-01B-01D-0563-05",
        "TCGA-20-1682-01A-01D-0563-05",
        "TCGA-20-1683-01A-01D-0563-05",
        "TCGA-20-1684-01A-01D-0563-05",
        "TCGA-20-1685-01A-01D-0563-05",
        "TCGA-20-1686-01A-01D-0563-05",
        "TCGA-20-1687-01A-01D-0563-05",
        "TCGA-23-1114-01B-01D-0563-05",
        "TCGA-23-1809-01A-01D-0563-05",
        "TCGA-24-1847-01A-01D-0563-05",
        "TCGA-29-1688-01A-01D-0563-05",
        "TCGA-29-1690-01A-01D-0563-05",
        "TCGA-29-1691-01A-01D-0563-05",
        "TCGA-29-1693-01A-01D-0563-05",
        "TCGA-29-1694-01A-01D-0563-05",
        "TCGA-29-1695-01A-01D-0563-05",
        "TCGA-29-1696-01A-01D-0563-05",
        "TCGA-29-1697-01A-01D-0563-05",
        "TCGA-29-1698-01A-01D-0563-05",
        "TCGA-29-1699-01A-01D-0563-05",
        "TCGA-29-1701-01A-01D-0563-05",
        "TCGA-29-1702-01A-01D-0563-05",
        "TCGA-29-1703-01A-01D-0563-05",
        "TCGA-29-1705-01A-01D-0563-05",
        "TCGA-29-1707-01A-01D-0563-05"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "calculatePermutedScoreByGeneSampling",
      "title": "Calculate the permuted latent trait by gene sampling",
      "topics": [
        "calculatePermutedScoreByGeneSampling"
      ]
    },
    {
      "page": "computeAbility",
      "title": "Calculate latent traits for a given response matrix and item parameters using MLE",
      "topics": [
        "computeAbility"
      ]
    },
    {
      "page": "dichotomize",
      "title": "A wrapper that is able to dichotomize expression, methylation and CN data",
      "topics": [
        "dichotomize"
      ]
    },
    {
      "page": "dichotomizeCN",
      "title": "Dichotomizing copy number data based on segmented data (i.e. log2ratio).",
      "topics": [
        "dichotomizeCN"
      ]
    },
    {
      "page": "dichotomizeExpr",
      "title": "Dichotomize the expression data given both tumor and normal samples.",
      "topics": [
        "dichotomizeExpr"
      ]
    },
    {
      "page": "dichotomizeMethy",
      "title": "Dichotomize the methylation data given both tumor and normal controls.",
      "topics": [
        "dichotomizeMethy"
      ]
    },
    {
      "page": "fitOnSinglePlat",
      "title": "Fit IRT model on a single platform",
      "topics": [
        "fitOnSinglePlat"
      ]
    },
    {
      "page": "intIRTeasyRun",
      "title": "The easyrun function for integrating multiple modalities of high throughput assays using binary input matrix.",
      "topics": [
        "intIRTeasyRun"
      ]
    },
    {
      "page": "intIRTeasyRunFromRaw",
      "title": "The easyrun function for integrating multiple modalities of high throughput assays using raw data.",
      "topics": [
        "intIRTeasyRunFromRaw"
      ]
    },
    {
      "page": "datasets",
      "title": "Ovarian Cancer Datasets",
      "topics": [
        "CN_N",
        "CN_T",
        "Expr_N",
        "Expr_T",
        "Methy_N",
        "Methy_T",
        "OV"
      ]
    },
    {
      "page": "simulateBinaryResponseMat",
      "title": "Simulate binary response matrix according to 2-parameter Item Characteristic Function for given latent traits and item parameters.",
      "topics": [
        "simulateBinaryResponseMat"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "admisc",
    "cli",
    "codetools",
    "doParallel",
    "expm",
    "foreach",
    "generics",
    "glue",
    "iterators",
    "lattice",
    "lifecycle",
    "ltm",
    "magrittr",
    "MASS",
    "Matrix",
    "mclust",
    "msm",
    "mvtnorm",
    "pillar",
    "pkgconfig",
    "polycor",
    "rlang",
    "survival",
    "tibble",
    "utf8",
    "vctrs"
  ],
  "_vignettes": [
    {
      "source": "integIRTy.Rnw",
      "filename": "integIRTy.pdf",
      "title": "integIRTy Vignette",
      "engine": "utils::Sweave",
      "headings": [
        "Introduction",
        "A Quick Example",
        "Building The Pipeline Step By Step",
        "Parallelizing integIRTy",
        "File Location and Session Info"
      ],
      "created": "2017-07-11 20:47:45",
      "modified": "2017-07-11 20:47:45",
      "commits": 1
    }
  ],
  "_score": 2.4313637641589874,
  "_indexed": true,
  "_nocasepkg": "integirty",
  "_universes": [
    "cran"
  ],
  "_previous": "1.0.8",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.9",
      "date": "2026-09-25T01:48:52.000Z",
      "distro": "resolute",
      "commit": "1fc9f46b145b6b50188ec00f743f62906aa51670",
      "fileid": "https://r2.ropensci.org/0501b943693ebbf90ff84da4a213b80c088a26851b7624b1b4aba4d7c56675f0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/36083222998"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.9",
      "date": "2026-09-25T01:49:05.000Z",
      "distro": "resolute",
      "commit": "1fc9f46b145b6b50188ec00f743f62906aa51670",
      "fileid": "https://r2.ropensci.org/1aceff25c3f0c279bd4a3982cba6056e56de3b235b0fa2286db378678ab3bca8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/36083222998"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.9",
      "date": "2026-09-25T01:49:06.000Z",
      "commit": "1fc9f46b145b6b50188ec00f743f62906aa51670",
      "fileid": "https://r2.ropensci.org/475d2098d944ee27f588c00cec1a46953df41bebcce9aff4387ab8f921ce1d0d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/36083222998"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.9",
      "date": "2026-09-25T01:47:49.000Z",
      "commit": "1fc9f46b145b6b50188ec00f743f62906aa51670",
      "fileid": "https://r2.ropensci.org/e91ee2123ce71df13c96af297e1da877e632f317f03e92109e92b3c937ed26ab",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/36083222998"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0.9",
      "date": "2026-09-25T01:47:51.000Z",
      "commit": "1fc9f46b145b6b50188ec00f743f62906aa51670",
      "fileid": "https://r2.ropensci.org/ebaf80f0a0cbe19763cacc2a9aa5953e520074507273059a147da49c764a3f7a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/36083222998"
    }
  ]
}