{
  "_id": "6a1b04c01d7bb097a0a02a02",
  "Package": "trio",
  "Type": "Package",
  "Title": "Testing of SNPs and SNP Interactions in Case-Parent Trio Studies",
  "Version": "3.50.0",
  "Date": "2026-04-06",
  "Author": "Holger Schwender, Qing Li, Philipp Berger, Christoph Neumann,\nMargaret Taub, Ingo Ruczinski",
  "Maintainer": "Holger Schwender <holger.schw@gmx.de>",
  "Description": "Testing SNPs and SNP interactions with a genotypic TDT.\nThis package furthermore contains functions for computing\npairwise values of LD measures and for identifying LD blocks,\nas well as functions for setting up matched case pseudo-control\ngenotype data for case-parent trios in order to run trio logic\nregression, for imputing missing genotypes in trios, for\nsimulating case-parent trios with disease risk dependent on SNP\ninteraction, and for power and sample size calculation in trio\ndata.",
  "License": "LGPL-2",
  "biocViews": "SNP, GeneticVariability, Microarray, Genetics",
  "RoxygenNote": "7.3.3",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:03 UTC",
  "RemoteUrl": "https://github.com/bioc/trio",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "57269707193b661bcb06d70fa5fc0a78bc7a6139",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 10:41:53 UTC",
    "User": "root"
  },
  "MD5sum": "221856d51ba4835abb14fc30da469ea0",
  "_user": "bioc-release",
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  "_created": "2026-05-30T10:41:53.000Z",
  "_published": "2026-05-30T15:39:44.778Z",
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  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680460052",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/trio",
  "_commit": {
    "id": "57269707193b661bcb06d70fa5fc0a78bc7a6139",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
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    "geneticvariability",
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  ],
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_exports": [
    "addRefAlt",
    "allelicTDT",
    "colEMlrt",
    "colGxE",
    "colGxEPerms",
    "colGxG",
    "colGxGPerms",
    "colMAFtrio",
    "colNtrios",
    "colPOlrt",
    "colTAT",
    "colTDT",
    "colTDT2way",
    "colTDTebam",
    "colTDTinter2way",
    "colTDTmaxStat",
    "colTDTmaxTest",
    "colTDTsam",
    "combineNtrios",
    "combineNtriosList",
    "compPermTDT2way",
    "fastGxG",
    "fastGxGrec",
    "findLDblocks",
    "getGxEstats",
    "getLD",
    "getLDlarge",
    "getMatPseudo",
    "gtdt.ebam",
    "gtdt.stat",
    "lrControl",
    "ntrios2Dom",
    "ntrios2Rec",
    "orderSNPs",
    "ped2geno",
    "poly4root",
    "poly4rootMat",
    "probTDT",
    "qingEnv",
    "read.pedfile",
    "removeSNPs",
    "removeTrios",
    "scoreGxE",
    "scoreGxG",
    "scoreMaxStat",
    "scoreTDT",
    "splitBlocks",
    "tdt",
    "tdt2way",
    "tdtGxG",
    "trio.check",
    "trio.permTest",
    "trio.power",
    "trio.prepare",
    "trio.sim",
    "trioFS",
    "trioLR",
    "vcf2geno"
  ],
  "_datasets": [
    {
      "name": "freq.hap",
      "title": "Case-Parent Trio Data",
      "object": "trio.data",
      "file": "trio.data.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "key",
        "hap",
        "freq"
      ],
      "rows": 20,
      "table": true,
      "tojson": true
    },
    {
      "name": "LDdata",
      "title": "Case-Parent Trio Data",
      "object": "trio.data",
      "file": "trio.data.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "S1",
        "S2",
        "S3",
        "S4",
        "S5",
        "S6",
        "S7",
        "S8",
        "S9",
        "S10",
        "S11",
        "S12",
        "S13",
        "S14",
        "S15",
        "S16",
        "S17",
        "S18",
        "S19",
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        "S21",
        "S22",
        "S23",
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        "S31",
        "S32",
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        "S34",
        "S35",
        "S36",
        "S37",
        "S38",
        "S39",
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        "S41",
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        "S46",
        "S47",
        "S48",
        "S49",
        "S50"
      ],
      "rows": 500,
      "table": true,
      "tojson": true
    },
    {
      "name": "mat.test",
      "title": "Case-Parent Trio Data",
      "object": "trio.data",
      "file": "trio.data.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "SNP1",
        "SNP2",
        "SNP3",
        "SNP4",
        "SNP5",
        "SNP6"
      ],
      "rows": 300,
      "table": true,
      "tojson": true
    },
    {
      "name": "prob.mat.test",
      "title": "Case-Parent Trio Data",
      "object": "trio.data",
      "file": "trio.data.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": {},
      "rows": 334,
      "table": true,
      "tojson": true
    },
    {
      "name": "simuBkMap",
      "title": "Case-Parent Trio Data",
      "object": "trio.data",
      "file": "trio.data.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "key",
        "hap",
        "freq"
      ],
      "rows": 66,
      "table": true,
      "tojson": true
    },
    {
      "name": "step3way",
      "title": "Case-Parent Trio Data",
      "object": "trio.data",
      "file": "trio.data.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "trio.gen.err",
      "title": "Case-Parent Trio Data",
      "object": "trio.data",
      "file": "trio.data.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "famid",
        "pid",
        "snp1",
        "snp2",
        "snp3",
        "snp4",
        "snp5"
      ],
      "rows": 60,
      "table": true,
      "tojson": true
    },
    {
      "name": "trio.gen1",
      "title": "Case-Parent Trio Data",
      "object": "trio.data",
      "file": "trio.data.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "famid",
        "pid",
        "snp1",
        "snp2",
        "snp3",
        "snp4",
        "snp5",
        "snp6",
        "snp7",
        "snp8",
        "snp9",
        "snp10"
      ],
      "rows": 300,
      "table": true,
      "tojson": true
    },
    {
      "name": "trio.gen2",
      "title": "Case-Parent Trio Data",
      "object": "trio.data",
      "file": "trio.data.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "famid",
        "pid",
        "snp1",
        "snp2",
        "snp3",
        "snp4",
        "snp5",
        "snp6",
        "snp7",
        "snp8",
        "snp9",
        "snp10"
      ],
      "rows": 300,
      "table": true,
      "tojson": true
    },
    {
      "name": "trio.ped.err",
      "title": "Case-Parent Trio Data",
      "object": "trio.data",
      "file": "trio.data.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "famid",
        "pid",
        "fatid",
        "motid",
        "sex",
        "affected",
        "snp1_1",
        "snp1_2",
        "snp2_1",
        "snp2_2",
        "snp3_1",
        "snp3_2",
        "snp4_1",
        "snp4_2",
        "snp5_1",
        "snp5_2",
        "snp6_1",
        "snp6_2",
        "snp7_1",
        "snp7_2",
        "snp8_1",
        "snp8_2",
        "snp9_1",
        "snp9_2",
        "snp10_1",
        "snp10_2"
      ],
      "rows": 300,
      "table": true,
      "tojson": true
    },
    {
      "name": "trio.ped1",
      "title": "Case-Parent Trio Data",
      "object": "trio.data",
      "file": "trio.data.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "famid",
        "pid",
        "fatid",
        "motid",
        "sex",
        "affected",
        "snp1_1",
        "snp1_2",
        "snp2_1",
        "snp2_2",
        "snp3_1",
        "snp3_2",
        "snp4_1",
        "snp4_2",
        "snp5_1",
        "snp5_2",
        "snp6_1",
        "snp6_2",
        "snp7_1",
        "snp7_2",
        "snp8_1",
        "snp8_2",
        "snp9_1",
        "snp9_2",
        "snp10_1",
        "snp10_2"
      ],
      "rows": 300,
      "table": true,
      "tojson": true
    },
    {
      "name": "trio.ped2",
      "title": "Case-Parent Trio Data",
      "object": "trio.data",
      "file": "trio.data.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "famid",
        "pid",
        "fatid",
        "motid",
        "sex",
        "affected",
        "snp1_1",
        "snp1_2",
        "snp2_1",
        "snp2_2",
        "snp3_1",
        "snp3_2",
        "snp4_1",
        "snp4_2",
        "snp5_1",
        "snp5_2",
        "snp6_1",
        "snp6_2",
        "snp7_1",
        "snp7_2",
        "snp8_1",
        "snp8_2",
        "snp9_1",
        "snp9_2",
        "snp10_1",
        "snp10_2"
      ],
      "rows": 300,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "allelicTDT",
      "title": "Allelic TDT",
      "topics": [
        "allelicTDT",
        "print.aTDT"
      ]
    },
    {
      "page": "colEMlrt",
      "title": "EM Likelihood Ratio Test",
      "topics": [
        "colEMlrt",
        "print.colEMlrt"
      ]
    },
    {
      "page": "colGxE",
      "title": "Genotypic TDT for Gene-Environment Interactions",
      "topics": [
        "colGxE",
        "colGxEPerms"
      ]
    },
    {
      "page": "colGxGPerms",
      "title": "Permutation-Based gTDT for Two-Way Interactions",
      "topics": [
        "colGxGPerms",
        "compPermTDT2way"
      ]
    },
    {
      "page": "colNtrios",
      "title": "Frequency of Genotype Combinations",
      "topics": [
        "addRefAlt",
        "colNtrios",
        "print.tabNtrios"
      ]
    },
    {
      "page": "colPOlrt",
      "title": "Parent-of-Origin Tests",
      "topics": [
        "colPOlrt",
        "colTAT",
        "print.polrt",
        "print.tat"
      ]
    },
    {
      "page": "colTDTmaxTest",
      "title": "Maximum Genotypic TDT",
      "topics": [
        "colTDTmaxStat",
        "colTDTmaxTest",
        "print.maxStatTrio",
        "print.maxTestTrio"
      ]
    },
    {
      "page": "colTDTsam",
      "title": "SAM and EBAM for Trio Data",
      "topics": [
        "colTDTebam",
        "colTDTsam",
        "gtdt.ebam",
        "gtdt.stat"
      ]
    },
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