{
  "_id": "6a1057d9acfb0bcc41ca3161",
  "Package": "SIP",
  "Type": "Package",
  "Title": "Single-Iteration Permutation for Large-Scale Biobank Data",
  "Version": "0.1.0",
  "Authors@R": "c(person(\"Aubrey\", \"Annis\", role = c(\"aut\", \"cre\"), email = \"acannis@umich.edu\"))",
  "Description": "A single, phenome-wide permutation of large-scale biobank\ndata. When a large number of phenotypes are analyzed in\nparallel, a single permutation across all phenotypes followed\nby genetic association analyses of the permuted data enables\nestimation of false discovery rates (FDRs) across the phenome.\nThese FDR estimates provide a significance criterion for\ninterpreting genetic associations in a biobank context. For the\nbasic permutation of unrelated samples, this package takes a\nsample-by-variable file with ID, genotypic covariates,\nphenotypic covariates, and phenotypes as input. For data with\nrelated samples, it also takes a file with sample pair-wise\nidentity-by-descent information. The function outputs a\npermuted sample-by-variable file ready for genome-wide\nassociation analysis. See Annis et al. (2021)\n<doi:10.21203/rs.3.rs-873449/v1> for details.",
  "URL": "https://github.com/acannis/SIP",
  "BugReports": "https://github.com/acannis/SIP/issues",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.2",
  "Config/testthat/edition": "3",
  "Repository": "https://acannis.r-universe.dev",
  "Date/Publication": "2025-11-06 19:55:18 UTC",
  "RemoteUrl": "https://github.com/acannis/sip",
  "RemoteRef": "HEAD",
  "RemoteSha": "3fc04d1816045be0a42d3ba8b6da3cbaa571c99b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-09 07:10:07 UTC",
    "User": "root"
  },
  "Author": "Aubrey Annis [aut, cre]",
  "Maintainer": "Aubrey Annis <acannis@umich.edu>",
  "MD5sum": "41c63cc6c5bd72345d8ca6f758bb7de4",
  "_user": "acannis",
  "_type": "src",
  "_file": "SIP_0.1.0.tar.gz",
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  "_created": "2026-05-09T07:10:07.000Z",
  "_published": "2026-05-22T13:19:21.652Z",
  "_distro": "noble",
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  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/acannis/sip",
  "_commit": {
    "id": "3fc04d1816045be0a42d3ba8b6da3cbaa571c99b",
    "author": "acannis <31316212+acannis@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #2 from mkleinsa/patch-1\n\nUpdate DESCRIPTION",
    "time": 1762458918
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  "_maintainer": {
    "name": "Aubrey Annis",
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  "_usedby": 0,
  "_updates": [
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      "n": 4
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    {
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      "n": 3
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    "extra/readme.md",
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  "_realowner": "acannis",
  "_cranurl": true,
  "_releases": [
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      "date": "2025-12-11"
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      "rows": 10000,
      "table": true,
      "tojson": true
    },
    {
      "name": "sipPair_relatednessData",
      "title": "Single-iteration paired permutation relatedness data",
      "object": "sipPair_relatednessData",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "IID1",
        "IID2",
        "PropIBD"
      ],
      "rows": 9886,
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      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "get_fixed",
      "title": "This function subsets the sample-by-variable dataframe to the \"fixed\" (i.e., non-permuted) data. This subset should include ID variables, sex, and genotypic covariates.",
      "topics": [
        "get_fixed"
      ]
    },
    {
      "page": "get_pairPerm",
      "title": "This function samples individuals by pairs for permuting phenotype vectors in the paired-permutation function (sipPair.R)",
      "topics": [
        "get_pairPerm"
      ]
    },
    {
      "page": "get_pairPermDF",
      "title": "This function recombines the fixed data and permuted data in the paired-permutation function (sipPair.R) into a permuted sample-by-variable data frame.",
      "topics": [
        "get_pairPermDF"
      ]
    },
    {
      "page": "get_permDF",
      "title": "This function recombines the fixed data and permuted data into a permuted sample-by-variable data frame.",
      "topics": [
        "get_permDF"
      ]
    },
    {
      "page": "get_permIdx",
      "title": "This function samples indices for permuting phenotype vectors in the basic permutation function (sip.R) and for permuting leftover unpaired individuals in the paired-permutation function (sipPair.R).",
      "topics": [
        "get_permIdx"
      ]
    },
    {
      "page": "get_permute",
      "title": "This function subsets the sample-by-variable data frame to the permutable data. This subset should include phenotypes and phenotypic covariates.",
      "topics": [
        "get_permute"
      ]
    },
    {
      "page": "get_relCat",
      "title": "This function infers relatedness categories in the paired-permutation function (sip_pair.R) prior to permutation.",
      "topics": [
        "get_relCat"
      ]
    },
    {
      "page": "get_relPairs",
      "title": "This function pairs individuals in the paired-permutation function (sip_pair.R) into the most highly-related pairs possible.",
      "topics": [
        "get_relPairs"
      ]
    },
    {
      "page": "get_sexDF",
      "title": "This function divides the sample-by-variable data frame into males and females prior to permutation within sexes.",
      "topics": [
        "get_sexDF"
      ]
    },
    {
      "page": "get_singSamp",
      "title": "This function checks for uneven numbers of individuals within relatedness category and creates a data set for permuting single samples that will not be pair permuted (sip_pair.R).",
      "topics": [
        "get_singSamp"
      ]
    },
    {
      "page": "order_permDF",
      "title": "This function reorders the permuted sample-by-variable data frame to match the ID order of the primary sample-by-variable data frame.",
      "topics": [
        "order_permDF"
      ]
    },
    {
      "page": "phenotype_IBD_correlation",
      "title": "Phenotype-IBD correlation",
      "topics": [
        "phenotype_IBD_correlation"
      ]
    },
    {
      "page": "plot_phenotype_correlations",
      "title": "Phenotype correlation plot",
      "topics": [
        "plot_phenotype_correlations"
      ]
    },
    {
      "page": "sip",
      "title": "Single-iteration permutation for large-scale biobank data",
      "topics": [
        "sip"
      ]
    },
    {
      "page": "sip_exampleData",
      "title": "Single-iteration permutation phenotype and covariate data",
      "topics": [
        "sip_exampleData"
      ]
    },
    {
      "page": "sip_pair",
      "title": "Single-iteration paired permutation for large-scale biobank data with relatedness",
      "topics": [
        "sip_pair"
      ]
    },
    {
      "page": "sipPair_exampleData",
      "title": "Single-iteration paired permutation phenotype and covariate data",
      "topics": [
        "sipPair_exampleData"
      ]
    },
    {
      "page": "sipPair_relatednessData",
      "title": "Single-iteration paired permutation relatedness data",
      "topics": [
        "sipPair_relatednessData"
      ]
    }
  ],
  "_readme": "https://github.com/acannis/sip/raw/HEAD/README.md",
  "_rundeps": [
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    "cpp11",
    "data.table",
    "farver",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_score": 3.1760912590556813,
  "_indexed": true,
  "_nocasepkg": "sip",
  "_universes": [
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  ],
  "_binaries": [
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}