{
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  "Package": "KCsmart",
  "Type": "Package",
  "Title": "Multi sample aCGH analysis package using kernel convolution",
  "Version": "2.71.0",
  "Date": "2009-11-26",
  "Author": "Jorma de Ronde, Christiaan Klijn, Arno Velds",
  "Maintainer": "Jorma de Ronde <j.d.ronde@nki.nl>",
  "Description": "Multi sample aCGH analysis package using kernel\nconvolution",
  "License": "GPL-3",
  "Collate": "'AllClasses.R' 'access-methods.R' 'length-methods.R'\n'plot-methods.R' 'show-methods.R' 'sort-methods.R'\n'unlist-methods.R' 'write.table-methods.R' 'KC.R'",
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  "biocViews": "CopyNumberVariation, Visualization, aCGH, Microarray",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:33:23 UTC",
  "RemoteUrl": "https://github.com/bioc/KCsmart",
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    "type": "organization",
    "name": "Bioconductor",
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    "calcSpmCollection",
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    "findSigLevelFdr",
    "findSigLevelTrad",
    "getSigRegionsCompKC",
    "getSigSegments",
    "idPoints",
    "initialize",
    "plot",
    "plotScaleSpace",
    "show",
    "write.table"
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      "name": "hsMirrorLocs",
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      "file": "hsMirrorLocs.rda",
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      "object": "hsSampleData",
      "file": "hsSampleData.rda",
      "class": [
        "data.frame"
      ],
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        "sample 1",
        "sample 2",
        "sample 3",
        "sample 4",
        "sample 5",
        "sample 6",
        "sample 7",
        "sample 8",
        "sample 9",
        "sample 10",
        "sample 11",
        "sample 12",
        "sample 13",
        "sample 14",
        "sample 15",
        "sample 16",
        "sample 17",
        "sample 18",
        "sample 19",
        "sample 20"
      ],
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      "table": true,
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    {
      "name": "mmMirrorLocs",
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      "object": "mmMirrorLocs",
      "file": "mmMirrorLocs.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
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  ],
  "_help": [
    {
      "page": "KCsmart-package",
      "title": "KCsmart",
      "topics": [
        "KCsmart-package",
        "KCsmart"
      ]
    },
    {
      "page": "calcSpm",
      "title": "KCsmart wrapper",
      "topics": [
        "calcSpm"
      ]
    },
    {
      "page": "calcSpmCollection",
      "title": "KCsmart Comparative wrapper",
      "topics": [
        "calcSpmCollection"
      ]
    },
    {
      "page": "compareSpmCollection",
      "title": "KCsmart Comparative calculate null distribution",
      "topics": [
        "compareSpmCollection"
      ]
    },
    {
      "page": "compKc-class",
      "title": "KC smart comparative",
      "topics": [
        "compKc-class",
        "initialize,compKc-method",
        "plot,compKc-method",
        "show,compKc-method"
      ]
    },
    {
      "page": "compKcSigRegions-class",
      "title": "KC smart comparative",
      "topics": [
        "compKcSigRegions-class",
        "show,compKcSigRegions-method"
      ]
    },
    {
      "page": "findSigLevelFdr",
      "title": "This function has not been properly implemented yet",
      "topics": [
        "findSigLevelFdr"
      ]
    },
    {
      "page": "findSigLevelTrad",
      "title": "Find significance level",
      "topics": [
        "findSigLevelTrad"
      ]
    },
    {
      "page": "getSigRegionsCompKC",
      "title": "KCsmart Comparative calculate the signficant regions",
      "topics": [
        "getSigRegionsCompKC"
      ]
    },
    {
      "page": "getSigSegments",
      "title": "Retrieve the significantly gained and lost regions including the corresponding, original probes",
      "topics": [
        "getSigSegments"
      ]
    },
    {
      "page": "hsMirrorLocs",
      "title": "Mirror locations of the human genome",
      "topics": [
        "hsMirrorLocs"
      ]
    },
    {
      "page": "hsSampleData",
      "title": "Homo Sapiens artificial cgh data set",
      "topics": [
        "hsSampleData"
      ]
    },
    {
      "page": "idPoints",
      "title": "Identify points in sample point matrix plot",
      "topics": [
        "idPoints"
      ]
    },
    {
      "page": "KCData-class",
      "title": "Internal class \"KCData\"",
      "topics": [
        "KCData-class",
        "length,KCData-method",
        "unlist,KCData-method",
        "[[,KCData-method",
        "[[<-,KCData-method"
      ]
    },
    {
      "page": "KcghData-class",
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      "topics": [
        "initialize,KcghData-method",
        "KcghData-class",
        "sort,KcghData-method"
      ]
    },
    {
      "page": "KcghDataMirror-class",
      "title": "Class \"KcghDataMirror\"",
      "topics": [
        "initialize,KcghDataMirror-method",
        "KcghDataMirror-class"
      ]
    },
    {
      "page": "KcghDataSplit-class",
      "title": "Class \"KcghDataSplit\"",
      "topics": [
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        "KcghDataSplit-class"
      ]
    },
    {
      "page": "KcghDataSum-class",
      "title": "Class \"KcghDataSum\"",
      "topics": [
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        "KcghDataSum-class",
        "sort,KcghDataSum-method"
      ]
    },
    {
      "page": "mmMirrorLocs",
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      "topics": [
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    },
    {
      "page": "plot",
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      "topics": [
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        "plot,compKc,missing-method",
        "plot,samplePointMatrix,missing-method",
        "plot,scaleSpace,missing-method"
      ]
    },
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      "page": "plotScaleSpace",
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      "topics": [
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      "page": "probeAnnotation-class",
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        "probeAnnotation-class",
        "[,probeAnnotation-method"
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      "topics": [
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        "show,samplePointMatrix-method"
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    },
    {
      "page": "sigSegments-class",
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      "topics": [
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        "sigSegments-class"
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    },
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      "page": "spmCollection-class",
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      "topics": [
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        "spmCollection-class"
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    },
    {
      "page": "write.table",
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