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  "Title": "Association Between Methylation and a Phenotype of Interest",
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  "Date": "2024-07-15",
  "Author": "Barfield, R., Conneely, K., Kilaru,V",
  "Maintainer": "R Barfield <barfieldrichard8@gmail.com>",
  "Description": "Is designed to test for association between methylation at\nCpG sites across the genome and a phenotype of interest,\nadjusting for any relevant covariates. The package can perform\nstandard analyses of large datasets very quickly with no need\nto impute the data. It can also handle mixed effects models\nwith chip or batch entering the model as a random intercept.\nAlso includes tools to apply quality control filters, perform\npermutation tests, and create QQ plots, manhattan plots, and\nscatterplots for individual CpG sites.",
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  "NeedsCompilation": "no",
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    "User": "root"
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  "Repository": "https://rbarfield.r-universe.dev",
  "Date/Publication": "2024-07-17 02:45:10 UTC",
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    "email": "barfieldrichard8@gmail.com",
    "login": "rbarfield",
    "description": "Collaborative Biostatistician at Research Institute in North Carolina",
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    "extra/citation.json",
    "extra/citation.txt",
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    "manual.pdf"
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  "_realowner": "rbarfield",
  "_cranurl": false,
  "_releases": [
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      "date": "2012-05-22"
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      "date": "2012-05-26"
    },
    {
      "version": "1.3",
      "date": "2012-07-18"
    },
    {
      "version": "2.0",
      "date": "2013-09-16"
    },
    {
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      "date": "2014-01-10"
    },
    {
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      "date": "2015-01-28"
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      "date": "2016-01-29"
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      "date": "2017-05-30"
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    "cpg.everything.character",
    "cpg.everything.complex",
    "cpg.everything.logical",
    "cpg.everything.matrix",
    "cpg.everything.numeric",
    "cpg.GC",
    "cpg.length",
    "cpg.perm",
    "cpg.qc",
    "cpg.work",
    "cpgassocsummary",
    "design",
    "design.data.frame",
    "design.NULL",
    "manhattan",
    "manhattan.reflect",
    "plot.cpg",
    "plot.cpg.perm",
    "pointsizefunction",
    "print.cpg",
    "print.cpg.gc",
    "print.cpg.perm",
    "print.cpg.perm.gc",
    "scatterplot",
    "sort.cpg",
    "sort.cpg.perm",
    "summary.cpg",
    "summary.cpg.perm"
  ],
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      "title": "Sample data from 'CpGassoc'",
      "object": "annotation",
      "file": "annotation.rda",
      "class": [
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      ],
      "fields": [
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        "CHR",
        "MAPINFO"
      ],
      "rows": 1228,
      "table": true,
      "tojson": true
    },
    {
      "name": "samplecpg",
      "title": "Sample data from 'CpGassoc'",
      "object": "samplecpg",
      "file": "samplecpg.rda",
      "class": [
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        "array"
      ],
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      "rows": 1228,
      "table": true,
      "tojson": true
    },
    {
      "name": "samplepheno",
      "title": "Sample data from 'CpGassoc'",
      "object": "samplepheno",
      "file": "samplepheno.rda",
      "class": [
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      ],
      "fields": [
        "Dose",
        "SBP",
        "Distance",
        "weight",
        "Disease",
        "chip"
      ],
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      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "CpGassoc-package",
      "title": "Association Between Methylation and a Phenotype of Interest",
      "topics": [
        "CpGassoc-package",
        "CpGassoc"
      ]
    },
    {
      "page": "cpg.perm.object",
      "title": "Methods for object of class '\"cpg.perm\"'.",
      "topics": [
        "plot.cpg.perm",
        "print.cpg.perm",
        "sort.cpg.perm",
        "summary.cpg.perm"
      ]
    },
    {
      "page": "cpg",
      "title": "Methods for object of class '\"cpg\"'",
      "topics": [
        "plot.cpg",
        "print.cpg",
        "sort.cpg",
        "summary.cpg"
      ]
    },
    {
      "page": "cpg.assoc",
      "title": "Association Analysis Between Methylation Beta Values and Phenotype of Interest",
      "topics": [
        "cpg.assoc"
      ]
    },
    {
      "page": "cpg.combine",
      "title": "Combine various objects of class '\"cpg\"'",
      "topics": [
        "cpg.combine"
      ]
    },
    {
      "page": "cpg.everything",
      "title": "Multi-Task function",
      "topics": [
        "cpg.everything",
        "cpg.everything.character",
        "cpg.everything.complex",
        "cpg.everything.logical",
        "cpg.everything.matrix",
        "cpg.everything.numeric"
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      "page": "cpg.GC",
      "title": "cpg.GC and methods for output of function",
      "topics": [
        "cpg.GC",
        "print.cpg.gc",
        "print.cpg.perm.gc"
      ]
    },
    {
      "page": "cpg.perm",
      "title": "Perform a Permutation Test of the Association Between Methylation and a Phenotype of Interest",
      "topics": [
        "cpg.perm"
      ]
    },
    {
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      "topics": [
        "cpg.qc"
      ]
    },
    {
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      "title": "Does the analysis between the CpG sites and phenotype of interest",
      "topics": [
        "cpg.work"
      ]
    },
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      "title": "Create full and reduced design matrices for the cpg.assoc function.",
      "topics": [
        "design",
        "design.data.frame",
        "design.NULL"
      ]
    },
    {
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      "title": "Create a manhattan plot",
      "topics": [
        "manhattan"
      ]
    },
    {
      "page": "manhattan.reflect",
      "title": "Create a Reflective Manhattan plot",
      "topics": [
        "manhattan.reflect"
      ]
    },
    {
      "page": "other.functions",
      "title": "Information on miscellaneous other functions",
      "topics": [
        "cpg.length",
        "cpgassocsummary",
        "pointsizefunction"
      ]
    },
    {
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      "title": "Sample data from 'CpGassoc'",
      "topics": [
        "annotation",
        "samplecpg",
        "samplepheno"
      ]
    },
    {
      "page": "scatterplot",
      "title": "Plot beta values of individual CpG sites against the independent variable.",
      "topics": [
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      ]
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    "nlme"
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      "created": "2013-09-16 23:16:18",
      "modified": "2024-07-17 02:45:10",
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