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  "Type": "Package",
  "Title": "MAGAR: R-package to compute methylation Quantitative Trait Loci\n(methQTL) from DNA methylation and genotyping data",
  "Version": "1.21.0",
  "Date": "2024-11-13",
  "Authors@R": "c(\nperson(\"Michael\", \"Scherer\", email=\"michael.scherer@dkfz.de\", role=c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0001-7990-6179\"))\n)",
  "Description": "\"Methylation-Aware Genotype Association in R\" (MAGAR)\ncomputes methQTL from DNA methylation and genotyping data from\nmatched samples. MAGAR uses a linear modeling stragety to call\nCpGs/SNPs that are methQTLs. MAGAR accounts for the local\ncorrelation structure of CpGs.",
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  "_exports": [
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    "doImport",
    "doMethQTL",
    "doMethQTLChromosome",
    "filterPval",
    "getAnno",
    "getCorrelationBlocks",
    "getGeno",
    "getMethData",
    "getOverlappingQTL",
    "getOverlapUniverse",
    "getPheno",
    "getResult",
    "getResultGWASMap",
    "getSamples",
    "getSpecificQTL",
    "imputeMeth",
    "joinMethQTLResult",
    "loadMethQTLInput",
    "loadMethQTLResult",
    "overlapInputs",
    "overlapQTLs",
    "qtlAnnotationEnrichment",
    "qtlBaseSubstitutionEnrichment",
    "qtlDistanceScatterplot",
    "qtlGetOption",
    "qtlJSON2options",
    "qtlManhattanPlot",
    "qtlOptions2JSON",
    "qtlPlotBaseSubstitution",
    "qtlPlotClusterSize",
    "qtlPlotSNPCpGInteraction",
    "qtlSetOption",
    "qtlTFBSMotifEnrichment",
    "qtlUpsetPlot",
    "qtlUpSetPlotCorBlocks",
    "qtlUpSetPlotTagCpGs",
    "qtlVennPlot",
    "saveMethQTLInput",
    "saveMethQTLResult"
  ],
  "_help": [
    {
      "page": "computeCorrelationBlocks",
      "title": "computeCorrelationBlocks",
      "topics": [
        "computeCorrelationBlocks"
      ]
    },
    {
      "page": "doImport",
      "title": "doImport",
      "topics": [
        "doImport"
      ]
    },
    {
      "page": "doMethQTL",
      "title": "doMethQTL",
      "topics": [
        "doMethQTL"
      ]
    },
    {
      "page": "doMethQTLChromosome",
      "title": "doMethQTLChromosome",
      "topics": [
        "doMethQTLChromosome"
      ]
    },
    {
      "page": "filterPval",
      "title": "filterPval",
      "topics": [
        "filterPval",
        "filterPval,MethQTLResult-method"
      ]
    },
    {
      "page": "getAnno",
      "title": "getAnno",
      "topics": [
        "getAnno",
        "getAnno,methQTL-method",
        "getAnno,MethQTLInput-method",
        "getAnno,MethQTLResult-method"
      ]
    },
    {
      "page": "getCorrelationBlocks",
      "title": "getCorrelationBlocks",
      "topics": [
        "getCorrelationBlocks",
        "getCorrelationBlocks,MethQTLResult-method"
      ]
    },
    {
      "page": "getGeno",
      "title": "getGeno",
      "topics": [
        "getGeno",
        "getGeno,methQTL-method",
        "getGeno,MethQTLInput-method"
      ]
    },
    {
      "page": "getMethData",
      "title": "getMethData",
      "topics": [
        "getMethData",
        "getMethData,methQTL-method",
        "getMethData,MethQTLInput-method"
      ]
    },
    {
      "page": "getOverlappingQTL",
      "title": "getOverlappingQTL",
      "topics": [
        "getOverlappingQTL"
      ]
    },
    {
      "page": "getOverlapUniverse",
      "title": "getOverlapUniverse",
      "topics": [
        "getOverlapUniverse"
      ]
    },
    {
      "page": "getPheno",
      "title": "getPheno",
      "topics": [
        "getPheno",
        "getPheno,methQTL-method",
        "getPheno,MethQTLInput-method"
      ]
    },
    {
      "page": "getResult",
      "title": "getResult",
      "topics": [
        "getResult",
        "getResult,MethQTLResult-method"
      ]
    },
    {
      "page": "getResultGWASMap",
      "title": "getResultGWASMap",
      "topics": [
        "getResultGWASMap",
        "getResultGWASMap,MethQTLResult-method"
      ]
    },
    {
      "page": "getSamples",
      "title": "getSamples",
      "topics": [
        "getSamples",
        "getSamples,methQTL-method",
        "getSamples,MethQTLInput-method"
      ]
    },
    {
      "page": "getSpecificQTL",
      "title": "getSpecificQTL",
      "topics": [
        "getSpecificQTL"
      ]
    },
    {
      "page": "imputeMeth",
      "title": "imputeMeth",
      "topics": [
        "imputeMeth",
        "imputeMeth,methQTL-method",
        "imputeMeth,MethQTLInput-method"
      ]
    },
    {
      "page": "joinMethQTLResult",
      "title": "joinMethQTLResult",
      "topics": [
        "joinMethQTLResult"
      ]
    },
    {
      "page": "loadMethQTLInput",
      "title": "loadMethQTLInput",
      "topics": [
        "loadMethQTLInput"
      ]
    },
    {
      "page": "loadMethQTLResult",
      "title": "loadMethQTLResult",
      "topics": [
        "loadMethQTLResult"
      ]
    },
    {
      "page": "MethQTLInput-class",
      "title": "MethQTLInput-class",
      "topics": [
        "MethQTLInput-class"
      ]
    },
    {
      "page": "MethQTLResult-class",
      "title": "MethQTLResult-class",
      "topics": [
        "MethQTLResult-class"
      ]
    },
    {
      "page": "overlapInputs",
      "title": "overlapInputs",
      "topics": [
        "overlapInputs"
      ]
    },
    {
      "page": "overlapQTLs",
      "title": "overlapQTLs",
      "topics": [
        "overlapQTLs"
      ]
    },
    {
      "page": "QTL.OPTIONS",
      "title": "options.R",
      "topics": [
        "QTL.OPTIONS"
      ]
    },
    {
      "page": "qtlAnnotationEnrichment",
      "title": "qtlAnnotationEnrichment",
      "topics": [
        "qtlAnnotationEnrichment"
      ]
    },
    {
      "page": "qtlBaseSubstitutionEnrichment",
      "title": "qtlBaseSubstitutionEnrichment",
      "topics": [
        "qtlBaseSubstitutionEnrichment"
      ]
    },
    {
      "page": "qtlDistanceScatterplot",
      "title": "qtlDistanceScatterplot",
      "topics": [
        "qtlDistanceScatterplot"
      ]
    },
    {
      "page": "qtlGetOption",
      "title": "qtlGetOption Print the value of the global option",
      "topics": [
        "qtlGetOption"
      ]
    },
    {
      "page": "qtlJSON2options",
      "title": "qtlJSON2options",
      "topics": [
        "qtlJSON2options"
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    },
    {
      "page": "qtlManhattanPlot",
      "title": "qtlManhattanPlot",
      "topics": [
        "qtlManhattanPlot"
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    },
    {
      "page": "qtlOptions2JSON",
      "title": "qtlOptions2JSON",
      "topics": [
        "qtlOptions2JSON"
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    },
    {
      "page": "qtlPlotBaseSubstitution",
      "title": "qtlPlotBaseSubstitution",
      "topics": [
        "qtlPlotBaseSubstitution"
      ]
    },
    {
      "page": "qtlPlotClusterSize",
      "title": "qtlPlotClusterSize",
      "topics": [
        "qtlPlotClusterSize"
      ]
    },
    {
      "page": "qtlPlotSNPCpGInteraction",
      "title": "qtlPlotSNPCpGInteraction",
      "topics": [
        "qtlPlotSNPCpGInteraction"
      ]
    },
    {
      "page": "qtlSetOption",
      "title": "qtlSetOption",
      "topics": [
        "qtlSetOption"
      ]
    },
    {
      "page": "qtlTFBSMotifEnrichment",
      "title": "qtlTFBSMotifEnrichment",
      "topics": [
        "qtlTFBSMotifEnrichment"
      ]
    },
    {
      "page": "qtlUpsetPlot",
      "title": "qtlUpsetPlot",
      "topics": [
        "qtlUpsetPlot"
      ]
    },
    {
      "page": "qtlUpSetPlotCorBlocks",
      "title": "qtlUpSetPlotCorBlocks",
      "topics": [
        "qtlUpSetPlotCorBlocks"
      ]
    },
    {
      "page": "qtlUpSetPlotTagCpGs",
      "title": "qtlUpSetPlotTagCpGs",
      "topics": [
        "qtlUpSetPlotTagCpGs"
      ]
    },
    {
      "page": "qtlVennPlot",
      "title": "qtlVennPlot",
      "topics": [
        "qtlVennPlot"
      ]
    },
    {
      "page": "saveMethQTLInput",
      "title": "saveMethQTLInput",
      "topics": [
        "saveMethQTLInput",
        "saveMethQTLInput,methQTL-method",
        "saveMethQTLInput,MethQTLInput-method"
      ]
    },
    {
      "page": "saveMethQTLResult",
      "title": "saveMethQTLResult",
      "topics": [
        "saveMethQTLResult",
        "saveMethQTLResult,methQTL-method",
        "saveMethQTLResult,MethQTLResult-method"
      ]
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      "source": "MAGAR.Rmd",
      "filename": "MAGAR.html",
      "title": "MAGAR: Methylation-Aware Genotype Association in R",
      "author": "Michael Scherer",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "Installation",
        "Required external software tools",
        "Input data",
        "DNA methylation data (microarrays)",
        "Genotyping data",
        "PLINK files",
        "IDAT files",
        "Imputation",
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        "Lists of methQTL results",
        "Advanced configuration",
        "MAGAR options",
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      "created": "2020-09-29 10:28:06",
      "modified": "2021-10-20 12:40:31",
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