{
  "_id": "6ab24fbe3d719c1f8408b9cf",
  "Package": "aCGH",
  "Title": "Classes and functions for Array Comparative Genomic\nHybridization data",
  "Version": "1.90.0",
  "Date": "2010-04-15",
  "Author": "Jane Fridlyand <jfridlyand@cc.ucsf.edu>, Peter Dimitrov\n<dimitrov@stat.Berkeley.EDU>",
  "Description": "Functions for reading aCGH data from image analysis output\nfiles and clone information files, creation of aCGH S3 objects\nfor storing these data. Basic methods for accessing/replacing,\nsubsetting, printing and plotting aCGH objects.",
  "Maintainer": "Peter Dimitrov <dimitrov@stat.Berkeley.EDU>",
  "License": "GPL-2",
  "Collate": "aCGH.R aCGH.plotting.R aCGH.read.R aCGH.test.R clusterGenome.R\nfuncs.dataplot.R heatmap.R hmm.R human.chrom.info.Jul03.R\nhuman.chrom.info.May04.R mergeLevels.R",
  "LazyLoad": "yes",
  "biocViews": "CopyNumberVariation, DataImport, Genetics",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:30:39 UTC",
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  "_published": "2026-09-22T09:51:58.425Z",
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    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
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    "dataimport",
    "genetics",
    "cpp"
  ],
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    "extra/contents.json",
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    "aCGH.read.Sprocs",
    "aCGH.test",
    "changeProp.func",
    "changeProp.overall.func",
    "clone.names",
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    "clones.info",
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    "col.names.aCGH",
    "col.names<-.aCGH",
    "colnames.aCGH",
    "colnames<-.aCGH",
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    "computeSD.func",
    "computeSD.Samples",
    "corna",
    "create.aCGH",
    "create.resT",
    "dim.aCGH",
    "dotify.names",
    "extract.clones.info",
    "fga.func",
    "find.genomic.events",
    "find.hmm.states",
    "findAber.func",
    "findAmplif.func",
    "findOutliers.func",
    "findTrans.func",
    "floorFunc",
    "gainLoss",
    "genomic.events",
    "genomic.events<-",
    "heatmap",
    "hmm",
    "hmm.merged",
    "hmm.merged<-",
    "hmm.run.func",
    "hmm<-",
    "human.chrom.info.Jul03",
    "human.chrom.info.May04",
    "impute.HMM",
    "impute.lowess",
    "is.aCGH",
    "is.even",
    "is.odd",
    "lengthGain.na",
    "lengthLoss.na",
    "lengthNumFunc",
    "log2.ratios",
    "log2.ratios.imputed",
    "log2.ratios.imputed<-",
    "maPalette",
    "maxdiff.func",
    "maxna",
    "mergeFunc",
    "mergeHmmStates",
    "mergeLevels",
    "mincorr.func",
    "minna",
    "ncol.aCGH",
    "nrow.aCGH",
    "num.chromosomes",
    "num.clones",
    "num.samples",
    "phenotype",
    "phenotype<-",
    "plot.aCGH",
    "plotCGH.func",
    "plotCGH.hmm.func",
    "plotChrom",
    "plotChrom.grey.samples.func",
    "plotChrom.hmm.func",
    "plotChrom.samples.func",
    "plotfreq.givenstat.final.colors.func",
    "plotfreq.stat.chrom.final.func",
    "plotfreq.stat.final.func",
    "plotFreqStat",
    "plotFreqStatColors",
    "plotFreqStatGrey",
    "plotGene",
    "plotGeneSign",
    "plotGenome",
    "plotHmmStates",
    "plotHmmStatesNew",
    "plotSummaryProfile",
    "plotValChrom",
    "plotvalChrom.func",
    "plotValGenome",
    "print.aCGH",
    "prop.na",
    "propGain.na",
    "propLoss.na",
    "propNumFunc",
    "read.Sproc.files",
    "row.names.aCGH",
    "row.names<-.aCGH",
    "rownames.aCGH",
    "rownames<-.aCGH",
    "sample.names",
    "sample.names<-",
    "sd.samples",
    "sd.samples<-",
    "states.hmm.func",
    "subset.hmm",
    "subset.hmm.merged",
    "summarize.clones",
    "summary.aCGH",
    "table.bac.func",
    "threshold.func"
  ],
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      "name": "colorectal",
      "title": "Colorectal array CGH dataset",
      "object": "colorectal",
      "file": "colorectal.rda",
      "class": [
        "aCGH"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ex.acgh.hmm",
      "title": "Class aCGH",
      "object": "colorectal",
      "file": "colorectal.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    }
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  "_help": [
    {
      "page": "aCGH",
      "title": "Class aCGH",
      "topics": [
        "aCGH",
        "clone.names",
        "clone.names<-",
        "clones.info",
        "col.names.aCGH",
        "col.names<-.aCGH",
        "colnames.aCGH",
        "colnames<-.aCGH",
        "corna",
        "create.aCGH",
        "dim.aCGH",
        "ex.acgh.hmm",
        "floorFunc",
        "genomic.events",
        "genomic.events<-",
        "hmm",
        "hmm.merged",
        "hmm.merged<-",
        "hmm<-",
        "is.aCGH",
        "is.even",
        "is.odd",
        "lengthNumFunc",
        "log2.ratios",
        "log2.ratios.imputed",
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        "maxna",
        "minna",
        "ncol.aCGH",
        "nrow.aCGH",
        "num.chromosomes",
        "num.clones",
        "num.samples",
        "phenotype",
        "phenotype<-",
        "plot.aCGH",
        "print.aCGH",
        "propNumFunc",
        "row.names.aCGH",
        "row.names<-.aCGH",
        "rownames.aCGH",
        "rownames<-.aCGH",
        "sample.names",
        "sample.names<-",
        "sd.samples",
        "sd.samples<-",
        "subset.hmm",
        "subset.hmm.merged",
        "summary.aCGH",
        "[.aCGH"
      ]
    },
    {
      "page": "aCGH.process",
      "title": "Process data in aCGH object",
      "topics": [
        "aCGH.process"
      ]
    },
    {
      "page": "aCGH.read.Sprocs",
      "title": "Create object of class \"aCGH\" from Sproc files",
      "topics": [
        "aCGH.read.Sprocs",
        "dotify.names",
        "extract.clones.info",
        "maxdiff.func",
        "mincorr.func",
        "read.Sproc.files"
      ]
    },
    {
      "page": "aCGH.test",
      "title": "Testing association of aCGH clones with censored or continuous outcomes",
      "topics": [
        "aCGH.test",
        "mt.maxT",
        "mt.minP"
      ]
    },
    {
      "page": "clusterGenome",
      "title": "clustering and heatmap",
      "topics": [
        "clusterGenome",
        "plotChrom",
        "plotValChrom",
        "plotvalChrom.func",
        "plotValGenome"
      ]
    },
    {
      "page": "colorectal",
      "title": "Colorectal array CGH dataset",
      "topics": [
        "clones.info.ex",
        "colorectal",
        "log2.ratios.ex",
        "pheno.type.ex"
      ]
    },
    {
      "page": "computeSD.func",
      "title": "Function to estimate experimental variability of a sample",
      "topics": [
        "computeSD.func",
        "computeSD.Samples"
      ]
    },
    {
      "page": "fga.func",
      "title": "Function to compute fraction of genome altered for each sample",
      "topics": [
        "fga.func"
      ]
    },
    {
      "page": "find.genomic.events",
      "title": "Finds the genomic events associated with each of the array CGH samples",
      "topics": [
        "find.genomic.events"
      ]
    },
    {
      "page": "find.hmm.states",
      "title": "Determines states of the clones",
      "topics": [
        "as.matrix.dist",
        "find.hmm.states",
        "hmm.run.func",
        "plotCGH.hmm.func",
        "plotChrom.grey.samples.func",
        "plotChrom.hmm.func",
        "plotChrom.samples.func",
        "smoothData.func",
        "thresholdData.func"
      ]
    },
    {
      "page": "findAber.func",
      "title": "Function to determines focal aberrations",
      "topics": [
        "findAber.func"
      ]
    },
    {
      "page": "findAmplif.func",
      "title": "Function to determine high level amplifications",
      "topics": [
        "findAmplif.func"
      ]
    },
    {
      "page": "findOutliers.func",
      "title": "Function to identify outlier clones",
      "topics": [
        "findOutliers.func"
      ]
    },
    {
      "page": "findTrans.func",
      "title": "Funtion identifying the transitions",
      "topics": [
        "findTrans.func"
      ]
    },
    {
      "page": "gainLoss",
      "title": "Function to compute proportion of gains and losses for each clones",
      "topics": [
        "gainLoss"
      ]
    },
    {
      "page": "heatmap",
      "title": "Creates heatmap array CGH objects",
      "topics": [
        "heatmap"
      ]
    },
    {
      "page": "human.chrom.info.Jul03",
      "title": "Basic Chromosomal Information for UCSC Human Genome Assembly July 2003 freeze",
      "topics": [
        "human.chrom.info.Jul03"
      ]
    },
    {
      "page": "human.chrom.info.May04",
      "title": "Basic Chromosomal Information for UCSC Human Genome Assembly May 2004 freeze",
      "topics": [
        "human.chrom.info.May04"
      ]
    },
    {
      "page": "impute.HMM",
      "title": "Imputing log2 ratios using HMM",
      "topics": [
        "impute.HMM"
      ]
    },
    {
      "page": "impute.lowess",
      "title": "Imputing log2 ratios",
      "topics": [
        "impute.lowess"
      ]
    },
    {
      "page": "mergeFunc",
      "title": "Funtion to merge states based on their state means",
      "topics": [
        "mergeFunc",
        "mergeHmmStates"
      ]
    },
    {
      "page": "mergeLevels",
      "title": "mergeLevels",
      "topics": [
        "combine.func",
        "mergeLevels"
      ]
    },
    {
      "page": "plotFreqStat",
      "title": "frequency plots and significance analysis",
      "topics": [
        "changeProp.func",
        "changeProp.overall.func",
        "create.resT",
        "lengthGain.na",
        "lengthLoss.na",
        "plotfreq.givenstat.final.colors.func",
        "plotfreq.stat.chrom.final.func",
        "plotfreq.stat.final.func",
        "plotFreqGivenStat",
        "plotfreqGivenStatFinalColors",
        "plotFreqStat",
        "plotFreqStatColors",
        "plotFreqStatGrey",
        "prop.na",
        "propGain.na",
        "propLoss.na",
        "table.bac.func"
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    },
    {
      "page": "plotGenome",
      "title": "Plots the genome",
      "topics": [
        "maPalette",
        "plotCGH.func",
        "plotGene",
        "plotGeneSign",
        "plotGenome"
      ]
    },
    {
      "page": "plotHmmStates",
      "title": "Plotting the estimated hmm states and log2 ratios for each sample.",
      "topics": [
        "plotHmmStates",
        "plotHmmStatesNew"
      ]
    },
    {
      "page": "plotSummaryProfile",
      "title": "plotSummaryProfile",
      "topics": [
        "plotSummaryProfile"
      ]
    },
    {
      "page": "states.hmm.func",
      "title": "A function to fit unsupervised Hidden Markov model",
      "topics": [
        "states.hmm.func"
      ]
    },
    {
      "page": "summarize.clones",
      "title": "Extracting summary information for all clones",
      "topics": [
        "summarize.clones"
      ]
    },
    {
      "page": "threshold.func",
      "title": "Function to indicate gain or loss for each clone for each sample",
      "topics": [
        "threshold.func"
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    }
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      "source": "aCGH.Rnw",
      "filename": "aCGH.pdf",
      "title": "aCGH Overview",
      "engine": "utils::Sweave",
      "headings": [
        "Overview",
        "Data",
        "Examples",
        "Acknowledgements"
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      "created": "2013-11-01 19:51:51",
      "modified": "2013-11-01 19:51:51",
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