{
  "_id": "6a1f011eb401979e7341af63",
  "Package": "metaGE",
  "Title": "Meta-Analysis for Detecting Genotype x Environment Associations",
  "Version": "1.2.2",
  "Authors@R": "c(\nperson(\"Annaïg\", \"De Walsche\", , \"annaig.de-walsche@inrae.fr\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-0603-1716\")),\nperson(\"Tristan\", \"Mary-Huard\", , \"tristan.mary-huard@agroparistech.fr\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-3839-9067\"))\n)",
  "Maintainer": "Annaïg De Walsche <annaig.de-walsche@inrae.fr>",
  "Description": "Provides functions to perform all steps of genome-wide\nassociation meta-analysis for studying Genotype x Environment\ninteractions, from collecting the data to the manhattan plot.\nThe procedure accounts for the potential correlation between\nstudies. In addition to the Fixed and Random models, one can\ninvestigate the relationship between QTL effects and some\nqualitative or quantitative covariate via the test of contrast\nand the meta-regression, respectively.  The methodology is\navailable from: (De Walsche, A., et al. (2025)\n\\doi{10.1371/journal.pgen.1011553}).",
  "License": "GPL-3",
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  "Packaged": {
    "Date": "2026-05-18 08:31:13 UTC",
    "User": "root"
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  "Author": "Annaïg De Walsche [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-0603-1716>), Tristan Mary-Huard\n[aut] (ORCID: <https://orcid.org/0000-0002-3839-9067>)",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2025-07-21 12:30:07 UTC",
  "RemoteUrl": "https://github.com/cran/metaGE",
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      "date": "2023-03-08"
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    "metaGE.cor",
    "metaGE.fit",
    "metaGE.heatmap",
    "metaGE.incidence",
    "metaGE.lscore",
    "metaGE.manhattan",
    "metaGE.pvalplot",
    "metaGE.regplot",
    "metaGE.test"
  ],
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      "name": "envDesc",
      "title": "Description of the environments.",
      "object": "envDesc",
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        "tbl",
        "data.frame"
      ],
      "fields": [
        "ShortName",
        "Temp",
        "Water",
        "Classification",
        "Tnight.mean",
        "ET0.mean"
      ],
      "rows": 10,
      "table": true,
      "tojson": true
    },
    {
      "name": "metaData",
      "title": "Results of different GWAS.",
      "object": "metaData",
      "class": [
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        "tbl",
        "data.frame"
      ],
      "fields": [
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        "POS",
        "MARKER",
        "FREQ.Cam12R",
        "EFFECT.Cam12R",
        "PVAL.Cam12R",
        "ALLELE0",
        "ALLELE1",
        "FREQ.Cam12W",
        "EFFECT.Cam12W",
        "PVAL.Cam12W",
        "FREQ.Deb12R",
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        "FREQ.Gai12R",
        "EFFECT.Gai12R",
        "PVAL.Gai12R",
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        "PVAL.Gai12W",
        "FREQ.Kar12R",
        "EFFECT.Kar12R",
        "PVAL.Kar12R",
        "FREQ.Kar12W",
        "EFFECT.Kar12W",
        "PVAL.Kar12W",
        "FREQ.Ner12R",
        "EFFECT.Ner12R",
        "PVAL.Ner12R",
        "FREQ.Ner12W",
        "EFFECT.Ner12W",
        "PVAL.Ner12W"
      ],
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      "table": true,
      "tojson": true
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    {
      "page": "autocor",
      "title": "Computation of the autocorrelation",
      "topics": [
        "autocor"
      ]
    },
    {
      "page": "CheckContrast",
      "title": "Check and reformat the matrix of contrast",
      "topics": [
        "CheckContrast"
      ]
    },
    {
      "page": "CheckIncidence",
      "title": "Check and reformat the matrix of incidence",
      "topics": [
        "CheckIncidence"
      ]
    },
    {
      "page": "ContrastStatTest",
      "title": "Compute the statistic of the contrast test.",
      "topics": [
        "ContrastStatTest"
      ]
    },
    {
      "page": "ContrastStatTest.NA",
      "title": "Compute the statistic of the contrast test in presence of missing values",
      "topics": [
        "ContrastStatTest.NA"
      ]
    },
    {
      "page": "envDesc",
      "title": "Description of the environments.",
      "topics": [
        "envDesc"
      ]
    },
    {
      "page": "FastKerFdr",
      "title": "FastKerFdr",
      "topics": [
        "FastKerFdr"
      ]
    },
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      "title": "GetH0Items",
      "topics": [
        "GetH0Items"
      ]
    },
    {
      "page": "lindley",
      "title": "Computation of the lindley process from scores.",
      "topics": [
        "lindley"
      ]
    },
    {
      "page": "LLikelihoodT_vect",
      "title": "LLikelihoodT_vect",
      "topics": [
        "LLikelihoodT_vect"
      ]
    },
    {
      "page": "MakeQQplot",
      "title": "Drawing a QQplot",
      "topics": [
        "MakeQQplot"
      ]
    },
    {
      "page": "metaData",
      "title": "Results of different GWAS.",
      "topics": [
        "metaData"
      ]
    },
    {
      "page": "metaGE.collect",
      "title": "Collect the results of GWAS data from different files",
      "topics": [
        "metaGE.collect"
      ]
    },
    {
      "page": "metaGE.cor",
      "title": "Infer inter-environment correlation matrix",
      "topics": [
        "metaGE.cor"
      ]
    },
    {
      "page": "metaGE.fit",
      "title": "Meta-analysis procedure: Fixed or Random effect.",
      "topics": [
        "metaGE.fit"
      ]
    },
    {
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      "title": "Draw the heatmap to see markers effects across environments.",
      "topics": [
        "metaGE.heatmap"
      ]
    },
    {
      "page": "metaGE.incidence",
      "title": "Create the matrix of incidence.",
      "topics": [
        "metaGE.incidence"
      ]
    },
    {
      "page": "metaGE.lscore",
      "title": "Compute the local score from a set of pvalues.",
      "topics": [
        "metaGE.lscore"
      ]
    },
    {
      "page": "metaGE.manhattan",
      "title": "Draw the Manhattan plot.",
      "topics": [
        "metaGE.manhattan"
      ]
    },
    {
      "page": "metaGE.pvalplot",
      "title": "Display visual checks of pvalues.",
      "topics": [
        "metaGE.pvalplot"
      ]
    },
    {
      "page": "metaGE.regplot",
      "title": "Plot the z-score of a marker according to a covariate.",
      "topics": [
        "metaGE.regplot"
      ]
    },
    {
      "page": "metaGE.test",
      "title": "Meta-analysis test for Genotype x Environment interactions: Contrast or Regression.",
      "topics": [
        "metaGE.test"
      ]
    },
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      "title": "ReadData",
      "topics": [
        "ReadData"
      ]
    },
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      "title": "Compute the pvalue of the meta-regression test.",
      "topics": [
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      "author": "Annaig De Walsche",
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        "Tests for  GxE interactions",
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