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  "Package": "CNVrd2",
  "Type": "Package",
  "Title": "CNVrd2: a read depth-based method to detect and genotype complex\ncommon copy number variants from next generation sequencing\ndata.",
  "Version": "1.50.0",
  "Date": "2014-10-04",
  "Author": "Hoang Tan Nguyen, Tony R Merriman and Mik Black",
  "VignetteBuilder": "knitr",
  "Maintainer": "Hoang Tan Nguyen <hoangtannguyenvn@gmail.com>",
  "Description": "CNVrd2 uses next-generation sequencing data to measure\nhuman gene copy number for multiple samples, indentify SNPs\ntagging copy number variants and detect copy number polymorphic\ngenomic regions.",
  "License": "GPL-2",
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      "table": false,
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      "object": "fcgr3bMXL",
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      "class": [
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      ],
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      "table": false,
      "tojson": false
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      ],
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      "table": false,
      "tojson": true
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      "page": "CNVrd2-package",
      "title": "CNVrd2",
      "topics": [
        "CNVrd2-package"
      ]
    },
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      "page": "calculateLDSNPandCNV",
      "title": "calculateLDSNPandCNV",
      "topics": [
        "calculateLDSNPandCNV"
      ]
    },
    {
      "page": "ccl3l1data",
      "title": "Data of CCL3L1 gene (The 1000 Genomes Project)",
      "topics": [
        "ccl3l1data"
      ]
    },
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      "page": "clusteringCNVs-class",
      "title": "Class '\"clusteringCNVs\"'",
      "topics": [
        "clusteringCNVs-class",
        "emnormalCNV,clusteringCNVs-method",
        "groupCNVs,clusteringCNVs-method",
        "objectCluster",
        "searchGroupCNVs,clusteringCNVs-method"
      ]
    },
    {
      "page": "CNVrd2-class",
      "title": "Class '\"CNVrd2\"'",
      "topics": [
        "CNVrd2-class",
        "countReadInWindow,CNVrd2-method",
        "plotCNVrd2,CNVrd2-method"
      ]
    },
    {
      "page": "countReadInWindow",
      "title": "Obtain read counts in constant windows.",
      "topics": [
        "countReadInWindow"
      ]
    },
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      "title": "Method 'countReadInWindow'",
      "topics": [
        "countReadInWindow-methods"
      ]
    },
    {
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        "emnormalCNV"
      ]
    },
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      "title": "Method 'emnormalCNV'",
      "topics": [
        "emnormalCNV-methods"
      ]
    },
    {
      "page": "fcgr3bMXL",
      "title": "MXL population data (The 1000 Genomes Project)",
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        "allGroups",
        "bamFiles",
        "copynumberGroups",
        "fcgr3bMXL",
        "objectCNVrd2",
        "readCountMatrix",
        "resultSegment"
      ]
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    {
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      "title": "groupBayesianCNVs",
      "topics": [
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      "title": "Cluster segmentation scores into groups.",
      "topics": [
        "groupCNVs"
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    },
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      "topics": [
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    },
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      "title": "Identity polymorphic regions.",
      "topics": [
        "identifyPolymorphicRegion"
      ]
    },
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      "page": "identifyPolymorphicRegion-methods",
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        "identifyPolymorphicRegion-methods"
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    {
      "page": "plotCNVrd2",
      "title": "Plot traces of samples.",
      "topics": [
        "plotCNVrd2"
      ]
    },
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      "page": "plotCNVrd2-methods",
      "title": "Method 'plotCNVrd2'",
      "topics": [
        "plotCNVrd2-methods"
      ]
    },
    {
      "page": "plotPolymorphicRegion",
      "title": "Plot polymorphic regions.",
      "topics": [
        "plotPolymorphicRegion"
      ]
    },
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        "plotPolymorphicRegion-methods"
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