{
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  "Package": "copynumber",
  "Title": "Segmentation of Single- and Multi-Track Copy Number Data by\nPenalized Least Squares Regression (with hg38/mm10/mm39)",
  "Version": "2.0.0",
  "Authors@R": "c(\nperson(\"Gro\", \"Nilsen\", , \"gronilse@ifi.uio.no\", role = c(\"aut\", \"cre\")),\nperson(\"Knut\", \"Liestol\", role = \"aut\"),\nperson(\"Ole Christian\", \"Lingjaerde\", role = \"aut\"),\nperson(\"Igor\", \"Dolgalev\", , \"igor.dolgalev@nyumc.org\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-4451-126X\"))\n)",
  "Description": "Penalized least squares regression is applied to fit\npiecewise constant curves to copy number data to locate genomic\nregions of constant copy number. Procedures are available for\nindividual segmentation of each sample, joint segmentation of\nseveral samples and joint segmentation of the two data tracks\nfrom SNP-arrays. Several plotting functions are available for\nvisualization of the data and the segmentation results.",
  "License": "Artistic-2.0",
  "URL": "https://igordot.github.io/copynumber/",
  "BugReports": "https://github.com/igordot/copynumber/issues",
  "VignetteBuilder": "knitr",
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  "Repository": "https://igordot.r-universe.dev",
  "Date/Publication": "2026-09-03 15:54:04 UTC",
  "RemoteUrl": "https://github.com/igordot/copynumber",
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  "NeedsCompilation": "no",
  "Packaged": {
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    "User": "root"
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  "Author": "Gro Nilsen [aut, cre],\nKnut Liestol [aut],\nOle Christian Lingjaerde [aut],\nIgor Dolgalev [aut] (ORCID: <https://orcid.org/0000-0003-4451-126X>)",
  "Maintainer": "Gro Nilsen <gronilse@ifi.uio.no>",
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  "_created": "2026-09-16T11:16:55.000Z",
  "_published": "2026-09-30T04:53:31.075Z",
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    "plotGenome",
    "plotHeatmap",
    "plotSample",
    "selectSegments",
    "subsetData",
    "subsetSegments",
    "winsorize"
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      "title": "Artificial SNP array data",
      "object": "BAF",
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      ],
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        "pos",
        "S1",
        "S2"
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      "table": true,
      "tojson": true
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      "object": "lymphoma",
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      "object": "micma",
      "class": [
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      ],
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      "page": "copynumber-package",
      "title": "copynumber: Segmentation of Single- and Multi-Track Copy Number Data by Penalized Least Squares Regression (with hg38/mm10/mm39)",
      "topics": [
        "copynumber-package",
        "copynumber"
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      "title": "Allele-specific copy number segmentation.",
      "topics": [
        "aspcf"
      ]
    },
    {
      "page": "callAberrations",
      "title": "Call aberrations in segmented data",
      "topics": [
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      "page": "getGRangesFormat",
      "title": "Get segments on the GRanges format",
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      ]
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      "title": "Impute missing copy number values",
      "topics": [
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      "title": "Interpolation of pcf-estimates.",
      "topics": [
        "interpolate.pcf"
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    },
    {
      "page": "SNPdata",
      "title": "Artificial SNP array data",
      "topics": [
        "BAF",
        "logR"
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    },
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      "page": "lymphoma",
      "title": "3K aCGH data",
      "topics": [
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      "title": "Subset of 244K aCGH data",
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      "topics": [
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      "title": "Single-sample copy number segmentation.",
      "topics": [
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      "page": "pcfPlain",
      "title": "Plain single-sample copy number segmentation.",
      "topics": [
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      ]
    },
    {
      "page": "plotAberration",
      "title": "Plot areas with copy number aberrations",
      "topics": [
        "plotAberration"
      ]
    },
    {
      "page": "plotAllele",
      "title": "Plot SNP data and/or aspcf segmentation results",
      "topics": [
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      ]
    },
    {
      "page": "plotChrom",
      "title": "Plot copy number data and/or segmentation results by chromosome",
      "topics": [
        "plotChrom"
      ]
    },
    {
      "page": "plotCircle",
      "title": "Plot a circular genome with aberration frequencies and connections between genomic loci added.",
      "topics": [
        "plotCircle"
      ]
    },
    {
      "page": "plotFreq",
      "title": "Plot percentage of samples with an aberration at a genomic position",
      "topics": [
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    },
    {
      "page": "plotGamma",
      "title": "Plot segmentation results for several values of gamma",
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      ]
    },
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      "page": "plotGenome",
      "title": "Plot copy number data and/or segmentation results",
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    },
    {
      "page": "plotHeatmap",
      "title": "Plot copy number heatmap",
      "topics": [
        "plotHeatmap"
      ]
    },
    {
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      "title": "Plot copy number data and/or segmentation results by sample",
      "topics": [
        "plotSample"
      ]
    },
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      "title": "Select multipcf segments",
      "topics": [
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      "headings": [
        "Introduction",
        "Overview",
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        "Segmentation",
        "Segmentation tools",
        "Choose model parameters",
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        "Circle plot",
        "Heatmap",
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        "References"
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      "created": "2026-08-20 19:01:41",
      "modified": "2026-09-03 15:54:04",
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