{
  "_id": "6a1f20b5b401979e73420438",
  "Package": "MultiPhen",
  "Type": "Package",
  "Title": "A Package to Test for Multi-Trait Association",
  "Version": "2.0.4",
  "Date": "2026-03-17",
  "Author": "Lachlan Coin [aut, cre], Paul O'Reilly [aut], Yotsawat Pompyen\n[aut], Clive Hoggart [aut], Federico Calboli [aut]",
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  "Maintainer": "Lachlan Coin <l.coin@imb.uq.edu.au>",
  "Description": "Performs genetic association tests between SNPs\n(one-at-a-time) and multiple phenotypes (separately or in joint\nmodel).",
  "License": "GPL-2",
  "LazyLoad": "yes",
  "NeedsCompilation": "no",
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  "Repository": "https://cran.r-universe.dev",
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  "_assets": [
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    "mPhen.assoc",
    "mPhen.cca",
    "mPhen.defineOptions",
    "mPhen.options",
    "mPhen.plotCorrelation",
    "mPhen.preparePheno",
    "mPhen.readGenotypes",
    "mPhen.readPhenoFiles",
    "mPhen.sampleCovar",
    "mPhen.sampleGeno",
    "mPhen.simulate",
    "mPhen.writeOutput",
    "read.plink"
  ],
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    {
      "name": "pheno",
      "title": "A dummy phenotype dataset that provides an example of the input phenotype data used by the package",
      "object": "pheno",
      "file": "pheno.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "testPheno1",
        "testPheno2",
        "testPheno3",
        "testPheno4",
        "testPheno5"
      ],
      "rows": 150,
      "table": true,
      "tojson": true
    },
    {
      "name": "snps",
      "title": "A dummy snp dataset that provides an example of the input snp data used by the package",
      "object": "snps",
      "file": "snps.imputed.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "1_1",
        "1_2",
        "1_3"
      ],
      "rows": 150,
      "table": true,
      "tojson": true
    },
    {
      "name": "snps.imputed",
      "title": "Imputed SNP dataset",
      "object": "snps.imputed",
      "file": "snps.imputed.rda",
      "class": [
        "array"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "MultiPhen-package",
      "title": "MultiPhen, a package for the genetic association testing of multiple phenotypes",
      "topics": [
        "MultiPhen-package",
        "MultiPhen"
      ]
    },
    {
      "page": "mPhen",
      "title": "A function for the genetic association testing of multiple phenotypes",
      "topics": [
        "mPhen"
      ]
    },
    {
      "page": "mPhen.assoc",
      "title": "A function for the genetic association testing of multiple phenotypes",
      "topics": [
        "mPhen.assoc"
      ]
    },
    {
      "page": "mPhen.cca",
      "title": "Sparse canonical correlation analysis",
      "topics": [
        "mPhen.cca"
      ]
    },
    {
      "page": "mPhen.defineOptions",
      "title": "Defines and modifies options.",
      "topics": [
        "mPhen.defineOptions"
      ]
    },
    {
      "page": "mPhen.options",
      "title": "Retrieves default mPhen options, and descriptions.",
      "topics": [
        "mPhen.options"
      ]
    },
    {
      "page": "mPhen.plotCorrelation",
      "title": "Plots correlation between phenotype values conditional on genotype",
      "topics": [
        "mPhen.plotCorrelation"
      ]
    },
    {
      "page": "mPhen.preparePheno",
      "title": "Prepare phenotype data for analysis",
      "topics": [
        "mPhen.preparePheno"
      ]
    },
    {
      "page": "mPhen.readGenotypes",
      "title": "Open, and read from a read connection to a genotype file",
      "topics": [
        "mPhen.readGenotypes"
      ]
    },
    {
      "page": "mPhen.readPhenoFiles",
      "title": "Read and merge phenotype files",
      "topics": [
        "mPhen.readPhenoFiles"
      ]
    },
    {
      "page": "mPhen.sampleCovar",
      "title": "Generates a covariance matrix.",
      "topics": [
        "mPhen.sampleCovar"
      ]
    },
    {
      "page": "mPhen.sampleGeno",
      "title": "Sample genotypes",
      "topics": [
        "mPhen.sampleGeno"
      ]
    },
    {
      "page": "mPhen.simulate",
      "title": "Simulates phenotypes according to a correlation structure.",
      "topics": [
        "mPhen.simulate"
      ]
    },
    {
      "page": "mPhen.writeOutput",
      "title": "Prepares output files and plots from MultiPhen results",
      "topics": [
        "mPhen.writeOutput"
      ]
    },
    {
      "page": "pheno",
      "title": "A dummy phenotype dataset that provides an example of the input phenotype data used by the package",
      "topics": [
        "pheno"
      ]
    },
    {
      "page": "read.plink",
      "title": "A function to read (small) binary PLINK binary files in a R session",
      "topics": [
        "read.plink"
      ]
    },
    {
      "page": "snps",
      "title": "A dummy snp dataset that provides an example of the input snp data used by the package",
      "topics": [
        "snps"
      ]
    },
    {
      "page": "snps.imputed",
      "title": "Imputed SNP dataset",
      "topics": [
        "snps.imputed"
      ]
    }
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