{
  "_id": "6ac78b98de46216d5edd1fc4",
  "Package": "CNAnorm",
  "Version": "1.59.0",
  "Date": "2012-08-06",
  "Title": "A normalization method for Copy Number Aberration in cancer\nsamples",
  "Author": "Stefano Berri <sberri@illumina.com>, Henry M. Wood\n<H.M.Wood@leeds.ac.uk>, Arief Gusnanto <a.gusnanto@leeds.ac.uk>",
  "Maintainer": "Stefano Berri <sberri@illumina.com>",
  "Description": "Performs ratio, GC content correction and normalization of\ndata obtained using low coverage (one read every 100-10,000 bp)\nhigh troughput sequencing. It performs a \"discrete\"\nnormalization looking for the ploidy of the genome. It will\nalso provide tumour content if at least two ploidy states can\nbe found.",
  "License": "GPL-2",
  "Collate": "AllGenerics.R AllClasses.R dataFrame2object.R\nworkflowWrapper.R initialize-methods.R summary-methods.R\nsmoothseg.R bandsegment.R mixtureModel.R normalize.R\nlength-methods.R CNAnorm-accessors.R CNAnorm-methods.R\nData-methods.R makeDefaultGraphParamteres.R",
  "URL": "http://www.r-project.org,",
  "LazyLoad": "yes",
  "Packaged": {
    "Date": "2026-10-08 12:13:07 UTC",
    "User": "root"
  },
  "biocViews": "CopyNumberVariation, Sequencing, Coverage, Normalization,\nWholeGenome, DNASeq, GenomicVariation",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:35:53 UTC",
  "RemoteUrl": "https://github.com/bioc/CNAnorm",
  "RemoteRef": "HEAD",
  "RemoteSha": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4",
  "NeedsCompilation": "yes",
  "_user": "bioc",
  "_type": "src",
  "_file": "CNAnorm_1.59.0.tar.gz",
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  "_expires": "2027-01-16T12:24:54.000Z",
  "_created": "2026-10-08T12:13:07.000Z",
  "_published": "2026-10-08T12:24:56.032Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/37774993382",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 2,
    "warning": 5,
    "note": 11
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  "_upstream": "https://github.com/bioc/CNAnorm",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777379753
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  "_maintainer": {
    "name": "Stefano Berri",
    "email": "sberri@illumina.com"
  },
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  "_dependencies": [
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      "version": ">= 2.10.1",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "DNAcopy",
      "role": "Imports"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
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      "version": "1.59.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.58.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "copynumbervariation",
    "sequencing",
    "coverage",
    "normalization",
    "wholegenome",
    "dnaseq",
    "genomicvariation"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 474,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 502,
    "source": "https://www.bioconductor.org/packages/stats/bioc/CNAnorm"
  },
  "_mentions": 21,
  "_searchresults": 8,
  "_rbuild": "4.6.1",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/CNAnorm.html",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addDNACopy",
    "addSmooth",
    "arms",
    "chrs",
    "chrs<-",
    "CNAnormWorkflow",
    "dataFrame2object",
    "discreteNorm",
    "exportTable",
    "gcNorm",
    "peakPloidy",
    "plotGenome",
    "plotPeaks",
    "pos",
    "pos<-",
    "ratio",
    "ratio.n",
    "ratio.s",
    "ratio.s.n",
    "segMean",
    "segMean.n",
    "sugg.peaks",
    "sugg.ploidy",
    "valid.peaks",
    "valid.ploidy",
    "validation"
  ],
  "_datasets": [
    {
      "name": "CN",
      "title": "A CNAnorm object with information about most abundant ploidy states, obtained from data LS041.",
      "object": "CN",
      "file": "CN.RData",
      "class": [
        "CNAnorm"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "gPar",
      "title": "An object with the default graphical parameters",
      "object": "gPar",
      "file": "gPar.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "hg19_hs_ideogr",
      "title": "An object with the ideogram information for homo sapiens - hg19",
      "object": "hg19_hs_ideogr",
      "file": "hg19_hs_ideogr.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chrom",
        "chromStart",
        "chromEnd",
        "name",
        "gieStain"
      ],
      "rows": 862,
      "table": true,
      "tojson": true
    },
    {
      "name": "LS041",
      "title": "Mapped reads in tumor and matched blood for patient LS041",
      "object": "LS041",
      "file": "LS041.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Chr",
        "Pos",
        "Test",
        "Norm",
        "GC"
      ],
      "rows": 7262,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "addDNACopy-methods",
      "title": "Methods for Function addDNACopy in Package `CNAnorm'",
      "topics": [
        "addDNACopy",
        "addDNACopy,CNAnorm-method",
        "addDNACopy-methods"
      ]
    },
    {
      "page": "addSmooth-methods",
      "title": "Methods for Function addSmooth in Package `CNAnorm'",
      "topics": [
        "addSmooth",
        "addSmooth,CNAnorm-method",
        "addSmooth-methods"
      ]
    },
    {
      "page": "chrsAndpos-methods",
      "title": "Accessors methods for Function ratio in Package `CNAnorm'",
      "topics": [
        "arms",
        "arms,CNAnorm-method",
        "arms-methods",
        "chrs",
        "chrs-methods",
        "chrs<-",
        "chrs<--methods",
        "pos",
        "pos,CNAnorm-method",
        "pos-methods",
        "pos<-",
        "pos<--methods"
      ]
    },
    {
      "page": "CN",
      "title": "A CNAnorm object with information about most abundant ploidy states, obtained from data LS041.",
      "topics": [
        "CN"
      ]
    },
    {
      "page": "CNAnorm-class",
      "title": "Class \"CNAnorm\"",
      "topics": [
        "chrs,CNAnorm-method",
        "chrs<-,CNAnorm-method",
        "CNAnorm",
        "CNAnorm-class",
        "length,CNAnorm-method",
        "pos<-,CNAnorm-method",
        "ratio,CNAnorm-method",
        "ratio.n,CNAnorm-method",
        "ratio.s,CNAnorm-method",
        "ratio.s.n,CNAnorm-method",
        "segMean,CNAnorm-method",
        "segMean.n,CNAnorm-method",
        "sugg.peaks,CNAnorm-method",
        "sugg.ploidy,CNAnorm-method",
        "valid.peaks,CNAnorm-method",
        "valid.ploidy,CNAnorm-method",
        "[,CNAnorm-method"
      ]
    },
    {
      "page": "workflowWrapper",
      "title": "Wrapper to '\"CNAnorm\"' workflow",
      "topics": [
        "CNAnormWorkflow"
      ]
    },
    {
      "page": "dataFrame2object",
      "title": "Convert a data frame into an object of Class '\"CNAnorm\"'",
      "topics": [
        "dataFrame2object"
      ]
    },
    {
      "page": "DerivData-class",
      "title": "Class \"DerivData\"",
      "topics": [
        "DerivData-class",
        "length,DerivData-method"
      ]
    },
    {
      "page": "discreteNorm-methods",
      "title": "Methods for Function addSmooth in Package `CNAnorm'",
      "topics": [
        "discreteNorm",
        "discreteNorm,CNAnorm-method",
        "discreteNorm-methods"
      ]
    },
    {
      "page": "exportTable-method",
      "title": "Methods for Function exportTable in Package `CNAnorm'",
      "topics": [
        "exportTable",
        "exportTable,CNAnorm-method",
        "exportTable-methods"
      ]
    },
    {
      "page": "gcNorm-methods",
      "title": "Methods for Function gcNorm in Package `CNAnorm'",
      "topics": [
        "gcNorm",
        "gcNorm,CNAnorm-method",
        "gcNorm-methods"
      ]
    },
    {
      "page": "gPar",
      "title": "An object with the default graphical parameters",
      "topics": [
        "gPar"
      ]
    },
    {
      "page": "data-hg19_hs_ideogr",
      "title": "An object with the ideogram information for homo sapiens - hg19",
      "topics": [
        "hg19_hs_ideogr"
      ]
    },
    {
      "page": "InData-class",
      "title": "Class \"InData\" ~~~",
      "topics": [
        "InData-class",
        "length,InData-method"
      ]
    },
    {
      "page": "LS041",
      "title": "Mapped reads in tumor and matched blood for patient LS041",
      "topics": [
        "LS041"
      ]
    },
    {
      "page": "Params-class",
      "title": "Class \"Params\"",
      "topics": [
        "Params-class"
      ]
    },
    {
      "page": "peakPloidy",
      "title": "Methods for Function peakPloidy in Package `CNAnorm'",
      "topics": [
        "peakPloidy",
        "peakPloidy,CNAnorm-method",
        "peakPloidy-methods"
      ]
    },
    {
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      "title": "Methods for Function plotGenome in Package `CNAnorm'",
      "topics": [
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        "plotGenome,CNAnorm-method",
        "plotGenome-methods"
      ]
    },
    {
      "page": "plotPeaks-methods",
      "title": "Methods for Function plotPeaks in Package `CNAnorm'",
      "topics": [
        "plotPeaks",
        "plotPeaks,CNAnorm-method",
        "plotPeaks-methods"
      ]
    },
    {
      "page": "ratio-methods",
      "title": "Methods for Function ratio in Package `CNAnorm'",
      "topics": [
        "ratio",
        "ratio-methods",
        "ratio.n",
        "ratio.n-methods",
        "ratio.s",
        "ratio.s-methods",
        "ratio.s.n",
        "ratio.s.n-methods",
        "segMean",
        "segMean-methods",
        "segMean.n",
        "segMean.n-methods"
      ]
    },
    {
      "page": "suggValid-methods",
      "title": "Methods for Function to retrieve suggested/validated ploidy and peaks in Package `CNAnorm'",
      "topics": [
        "sugg.peaks",
        "sugg.peaks-methods",
        "sugg.ploidy",
        "sugg.ploidy-methods",
        "valid.peaks",
        "valid.peaks-methods",
        "valid.ploidy",
        "valid.ploidy-methods"
      ]
    },
    {
      "page": "validation-methods",
      "title": "Methods for Function addSmooth in Package `CNAnorm'",
      "topics": [
        "validation",
        "validation,CNAnorm-method",
        "validation-methods"
      ]
    }
  ],
  "_rundeps": [
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      "source": "CNAnorm.Snw",
      "filename": "CNAnorm.pdf",
      "title": "An introduction to CNAnorm",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 20:21:19",
      "modified": "2014-03-05 16:55:42",
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  "_nocasepkg": "cnanorm",
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