{
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  "Package": "oligoClasses",
  "Version": "1.75.0",
  "Title": "Classes for high-throughput arrays supported by oligo and crlmm",
  "Author": "Benilton Carvalho and Robert Scharpf",
  "Maintainer": "Benilton Carvalho <beniltoncarvalho@gmail.com> and Robert\nScharpf <rscharpf@jhsph.edu>",
  "Description": "This package contains class definitions, validity checks,\nand initialization methods for classes used by the oligo and\ncrlmm packages.",
  "License": "GPL (>= 2)",
  "LazyLoad": "yes",
  "Collate": "AllClasses.R AllGenerics.R utils-general.R utils-lds.R\nutils-parallel.R methods-gSet.R initialize-methods.R\nmethods-AlleleSet.R methods-AnnotatedDataFrame.R\nmethods-FeatureSet.R methods-AssayData.R\nmethods-SnpFeatureSet.R methods-oligoSnpSet.R\nmethods-CopyNumberSet.R methods-CNSet.R methods-PDInfo.R\nmethods-RangedDataCNV.R methods-SnpSet.R\nmethods-GenomeAnnotatedDataFrame.R methods-BeadStudioSet.R\nmethods-BeadStudioSetList.R methods-gSetList.R\nmethods-GRanges.R methods-SummarizedExperiment.R show-methods.R\nfunctions.R zzz.R",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:32:32 UTC",
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    "A<-",
    "affyPlatforms",
    "allele",
    "annotatedDataFrameFrom",
    "annotation",
    "annotationPackages",
    "assayDataList",
    "AssayDataList",
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    "B<-",
    "baf",
    "baf<-",
    "batch",
    "batchNames",
    "batchNames<-",
    "batchStatistics",
    "batchStatistics<-",
    "bothStrands",
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    "calls<-",
    "celfileDate",
    "celfileName",
    "checkExists",
    "checkOrder",
    "chromosome",
    "chromosome<-",
    "chromosome2integer",
    "chromosomePositionOrder",
    "clone2",
    "close",
    "closeff",
    "cnConfidence",
    "cnConfidence<-",
    "coerce",
    "confs",
    "confs<-",
    "copyNumber",
    "copyNumber<-",
    "coverage2",
    "createFF",
    "db",
    "delCluster",
    "dims",
    "elementNROWS",
    "exprs",
    "featureDataList",
    "featuresInRange",
    "findOverlaps",
    "flags",
    "GenomeAnnotatedDataFrameFrom",
    "genomeBuild",
    "genomeBuild<-",
    "geometry",
    "getA",
    "getArm",
    "getBar",
    "getCluster",
    "getM",
    "getSequenceLengths",
    "i2p",
    "initialize",
    "initializeBigArray",
    "initializeBigMatrix",
    "initializeBigVector",
    "integer2chromosome",
    "integerArray",
    "integerMatrix",
    "is.ffmatrix",
    "isPackageLoaded",
    "isSnp",
    "kind",
    "ldPath",
    "ldSetOptions",
    "ldStatus",
    "library2",
    "list.celfiles",
    "lrr",
    "lrr<-",
    "makeFeatureGRanges",
    "manufacturer",
    "mean",
    "nu",
    "numberProbes",
    "ocLapply",
    "ocProbesets",
    "ocSamples",
    "open",
    "openff",
    "p2i",
    "parStatus",
    "pdPkgFromBioC",
    "phi",
    "position",
    "position<-",
    "requireAnnotation",
    "requireClusterPkg",
    "requireClusterPkgSet",
    "sampleNames",
    "sampleNames<-",
    "setCluster",
    "show",
    "splitIndicesByLength",
    "splitIndicesByNode",
    "state",
    "updateObject"
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    {
      "name": "efsExample",
      "title": "ExpressionFeatureSet Object",
      "object": "efsExample",
      "file": "efsExample.rda",
      "class": [
        "ExpressionFeatureSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "locusLevelData",
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      "file": "locusLevelData.rda",
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      "name": "oligoSet",
      "title": "An example instance of oligoSnpSet class",
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      "class": [
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      "class": [
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      "page": "affyPlatforms",
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    {
      "page": "AlleleSet-class",
      "title": "Class \"AlleleSet\"",
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        "allele,AlleleSet-method",
        "allele,SnpFeatureSet-method",
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        "batchNames<-,AssayData-method",
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        "batchNames",
        "batchNames<-"
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    {
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      "title": "Accessor for batch statistics uses for copy number estimation and storage of model parameters",
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        "batchStatistics",
        "batchStatistics<-"
      ]
    },
    {
      "page": "BeadStudioSet-class",
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      "topics": [
        "baf,BeadStudioSet-method",
        "baf<-",
        "baf<-,BeadStudioSet-method",
        "BafLrrSet-class",
        "BeadStudioSet",
        "BeadStudioSet-class",
        "coerce,BeadStudioSet,data.frame-method",
        "copyNumber,BeadStudioSet-method",
        "copyNumber<-,BeadStudioSet,ANY-method",
        "initialize,BeadStudioSet-method",
        "lrr,BeadStudioSet-method",
        "lrr<-",
        "lrr<-,BafLrrSet,ANY-method",
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        "lrr<-,BeadStudioSet,ANY-method",
        "lrr<-,BeadStudioSet-method",
        "show,BeadStudioSet-method",
        "updateObject,BeadStudioSet-method"
      ]
    },
    {
      "page": "BeadStudioSetList-class",
      "title": "List classes with assay data listed by chromosome",
      "topics": [
        "baf,BafLrrSetList-method",
        "baf,BeadStudioSetList-method",
        "baf,oligoSetList-method",
        "BafLrrSetList-class",
        "BeadStudioSetList-class",
        "calls,oligoSetList-method",
        "clone2",
        "clone2,BafLrrSetList-method",
        "copyNumber,oligoSetList-method",
        "initialize,BeadStudioSetList-method",
        "lrr,BafLrrSetList-method",
        "lrr,BeadStudioSetList-method",
        "lrr<-,BafLrrSetList,matrix-method",
        "oligoSetList-class",
        "updateObject,BeadStudioSetList-method",
        "[[,BafLrrSetList,ANY,ANY-method",
        "[[,BeadStudioSetList,ANY,ANY-method",
        "[[<-,BafLrrSetList,ANY,ANY,BafLrrSet-method"
      ]
    },
    {
      "page": "celfileDate",
      "title": "Cel file dates",
      "topics": [
        "celfileDate"
      ]
    },
    {
      "page": "celfileName",
      "title": "Extracts complete cel file name from a CNSet object",
      "topics": [
        "celfileName"
      ]
    },
    {
      "page": "checkExists",
      "title": "Checks to see whether an object exists and, if not, executes the appropriate function.",
      "topics": [
        "checkExists"
      ]
    },
    {
      "page": "checkOrder",
      "title": "Checks whether a eSet-derived class is ordered by chromosome and physical position",
      "topics": [
        "checkOrder",
        "chromosomePositionOrder"
      ]
    },
    {
      "page": "chromosome-methods",
      "title": "Methods for function chromosome in package oligoClasses",
      "topics": [
        "chromosome",
        "chromosome,AnnotatedDataFrame-method",
        "chromosome,GenomeAnnotatedDataFrame-method",
        "chromosome,GRanges-method",
        "chromosome,GRangesList-method",
        "chromosome,gSet-method",
        "chromosome,SnpSet-method",
        "chromosome-methods",
        "chromosome<-",
        "chromosome<-,GenomeAnnotatedDataFrame,integer-method",
        "chromosome<-,gSet,integer-method",
        "chromosome<-,SnpSet,integer-method"
      ]
    },
    {
      "page": "chromosome2integer",
      "title": "Converts chromosome to integer",
      "topics": [
        "chromosome2integer",
        "integer2chromosome"
      ]
    },
    {
      "page": "CNSet-class",
      "title": "Class \"CNSet\"",
      "topics": [
        "A,CNSet-method",
        "A<-,CNSet-method",
        "allele,CNSet-method",
        "B,CNSet-method",
        "B<-,CNSet-method",
        "batch,CNSet-method",
        "batchNames,CNSet-method",
        "batchNames<-,CNSet-method",
        "batchStatistics,CNSet-method",
        "batchStatistics<-,CNSet,AssayData-method",
        "calls,CNSet-method",
        "calls<-,CNSet,matrix-method",
        "close,CNSet-method",
        "CNSet",
        "CNSet-class",
        "coerce,CNSet,CopyNumberSet-method",
        "coerce,CNSet,oligoSnpSet",
        "coerce,CNSet,oligoSnpSet-method",
        "coerce,CNSetLM,CNSet-method",
        "confs,CNSet-method",
        "confs<-,CNSet,matrix-method",
        "corr,CNSet,character-method",
        "flags,CNSet-method",
        "initialize,CNSet-method",
        "initialize,CNSetLM-method",
        "nu,CNSet,character-method",
        "open,CNSet-method",
        "phi,CNSet,character-method",
        "show,CNSet-method",
        "sigma2,CNSet,character-method",
        "snpCallProbability,CNSet-method",
        "tau2,CNSet,character-method",
        "updateObject,CNSet-method",
        "[,CNSet,ANY-method",
        "[,CNSet-method"
      ]
    },
    {
      "page": "CopyNumberSet-class",
      "title": "Class '\"CopyNumberSet\"'",
      "topics": [
        "checkOrder,CopyNumberSet-method",
        "cnConfidence,CopyNumberSet-method",
        "cnConfidence<-,CopyNumberSet,matrix-method",
        "copyNumber,CopyNumberSet-method",
        "copyNumber<-,CopyNumberSet,matrix-method",
        "CopyNumberSet",
        "CopyNumberSet-class",
        "initialize,CopyNumberSet-method"
      ]
    },
    {
      "page": "CopyNumberSet-methods",
      "title": "Methods for class CopyNumberSet.",
      "topics": [
        "cnConfidence",
        "cnConfidence<-",
        "copyNumber",
        "copyNumber<-",
        "CopyNumberSet-methods"
      ]
    },
    {
      "page": "createFF",
      "title": "Create ff objects.",
      "topics": [
        "createFF"
      ]
    },
    {
      "page": "db",
      "title": "Get the connection to the SQLite Database",
      "topics": [
        "db",
        "db,DBPDInfo-method",
        "db,FeatureSet-method",
        "db,SnpCnvQSet-method",
        "db,SnpQSet-method",
        "db,SnpSet-method",
        "db-methods"
      ]
    },
    {
      "page": "DBPDInfo-class",
      "title": "Class \"DBPDInfo\"",
      "topics": [
        "AffyExonPDInfo",
        "AffyExonPDInfo-class",
        "AffyExpressionPDInfo",
        "AffyExpressionPDInfo-class",
        "AffyGenePDInfo",
        "AffyGenePDInfo-class",
        "AffySNPCNVPDInfo",
        "AffySNPCNVPDInfo-class",
        "AffySNPPDInfo",
        "AffySNPPDInfo-class",
        "AffySTPDInfo",
        "AffySTPDInfo-class",
        "AffyTilingPDInfo",
        "AffyTilingPDInfo-class",
        "annotation,DBPDInfo-method",
        "DBPDInfo",
        "DBPDInfo-class",
        "ExpressionPDInfo",
        "ExpressionPDInfo-class",
        "GenericPDInfo",
        "GenericPDInfo-class",
        "initialize,DBPDInfo-method",
        "NgsExpressionPDInfo",
        "NgsExpressionPDInfo-class",
        "NgsTilingPDInfo",
        "NgsTilingPDInfo-class",
        "show,DBPDInfo-method",
        "SNPCNVPDInfo",
        "SNPCNVPDInfo-class",
        "SNPPDInfo",
        "SNPPDInfo-class",
        "TilingPDInfo",
        "TilingPDInfo-class"
      ]
    },
    {
      "page": "data-efsExample",
      "title": "ExpressionFeatureSet Object",
      "topics": [
        "efsExample"
      ]
    },
    {
      "page": "exprs-methods",
      "title": "Accessor for the 'exprs' slot",
      "topics": [
        "exprs,FeatureSet-method",
        "exprs-methods",
        "se.exprs,FeatureSet-method"
      ]
    },
    {
      "page": "featureDataList-methods",
      "title": "Accessor for slot 'featureDataList' in Package 'oligoClasses' ~~",
      "topics": [
        "featureDataList",
        "featureDataList-methods"
      ]
    },
    {
      "page": "FeatureSetExtensions-class",
      "title": "\"FeatureSet\" and \"FeatureSet\" Extensions",
      "topics": [
        "ExonFeatureSet",
        "ExonFeatureSet-class",
        "ExpressionFeatureSet",
        "ExpressionFeatureSet-class",
        "FeatureSet",
        "FeatureSet-class",
        "GeneFeatureSet",
        "GeneFeatureSet-class",
        "GenericFeatureSet",
        "GenericFeatureSet-class",
        "initialize,FeatureSet-method",
        "show,FeatureSet-method",
        "SnpCnvFeatureSet",
        "SnpCnvFeatureSet-class",
        "SnpFeatureSet",
        "SnpFeatureSet-class",
        "TilingFeatureSet",
        "TilingFeatureSet-class",
        "TilingFeatureSet2",
        "TilingFeatureSet2-class"
      ]
    },
    {
      "page": "ff_matrix",
      "title": "Class \"ff_matrix\"",
      "topics": [
        "annotatedDataFrameFrom,ff_matrix-method",
        "ff_matrix-class"
      ]
    },
    {
      "page": "ff_or_matrix-class",
      "title": "Class '\"ff_or_matrix\"'",
      "topics": [
        "ff_or_matrix-class"
      ]
    },
    {
      "page": "ffdf",
      "title": "Class \"ffdf\"",
      "topics": [
        "ffdf-class",
        "list_or_ffdf-class"
      ]
    },
    {
      "page": "fileConnections",
      "title": "Open and close methods for matrices and numeric vectors",
      "topics": [
        "close",
        "close,array-method",
        "close,matrix-method",
        "close,numeric-method",
        "closeff",
        "closeff,CNSet-method",
        "open",
        "open,array-method",
        "open,matrix-method",
        "open,numeric-method",
        "openff",
        "openff,CNSet-method"
      ]
    },
    {
      "page": "flags",
      "title": "Batch-level summary of SNP flags.",
      "topics": [
        "flags"
      ]
    },
    {
      "page": "generics",
      "title": "Miscellaneous generics.  Methods defined in packages that depend on oligoClasses",
      "topics": [
        "baf",
        "lrr"
      ]
    },
    {
      "page": "GenomeAnnotatedDataFrame-class",
      "title": "Class '\"GenomeAnnotatedDataFrame\"'",
      "topics": [
        "coerce,AnnotatedDataFrame,GenomeAnnotatedDataFrame-method",
        "GenomeAnnotatedDataFrame",
        "GenomeAnnotatedDataFrame-class",
        "getArm,GenomeAnnotatedDataFrame-method",
        "initialize,GenomeAnnotatedDataFrame-method",
        "makeFeatureGRanges,GenomeAnnotatedDataFrame-method",
        "position<-",
        "position<-,GenomeAnnotatedDataFrame,integer-method",
        "updateObject,GenomeAnnotatedDataFrame-method"
      ]
    },
    {
      "page": "GenomeAnnotatedDataFrameFrom-methods",
      "title": "Methods for Function GenomeAnnotatedDataFrameFrom in Package oligoClasses",
      "topics": [
        "GenomeAnnotatedDataFrameFrom",
        "GenomeAnnotatedDataFrameFrom,array-method",
        "GenomeAnnotatedDataFrameFrom,AssayData-method",
        "GenomeAnnotatedDataFrameFrom,ff_or_matrix-method",
        "GenomeAnnotatedDataFrameFrom,list-method",
        "GenomeAnnotatedDataFrameFrom,NULL-method"
      ]
    },
    {
      "page": "genomeBuild",
      "title": "Genome Build Information",
      "topics": [
        "genomeBuild",
        "genomeBuild,DBPDInfo-method",
        "genomeBuild,FeatureSet-method",
        "genomeBuild<-"
      ]
    },
    {
      "page": "geometry-methods",
      "title": "Array Geometry Information",
      "topics": [
        "geometry",
        "geometry,DBPDInfo-method",
        "geometry,FeatureSet-method"
      ]
    },
    {
      "page": "AlleleSet-methods",
      "title": "Compute average log-intensities / log-ratios",
      "topics": [
        "A",
        "A,AlleleSet-method",
        "A<-",
        "A<-,AlleleSet,matrix-method",
        "A<-,AlleleSet-method",
        "B",
        "B,AlleleSet-method",
        "B<-",
        "B<-,AlleleSet,matrix-method",
        "B<-,AlleleSet-method",
        "close,AlleleSet-method",
        "getA",
        "getA,SnpCnvQSet-method",
        "getA,SnpQSet-method",
        "getA,TilingFeatureSet2-method",
        "getM",
        "getM,SnpCnvQSet-method",
        "getM,SnpQSet-method",
        "getM,TilingFeatureSet2-method",
        "open,AlleleSet-method"
      ]
    },
    {
      "page": "getBar",
      "title": "Gets a bar of a given length.",
      "topics": [
        "getBar"
      ]
    },
    {
      "page": "getSequenceLengths",
      "title": "Load chromosome sequence lengths for UCSC genome build hg18 or hg19",
      "topics": [
        "getSequenceLengths"
      ]
    },
    {
      "page": "GRanges-methods",
      "title": "Methods for GRanges objects",
      "topics": [
        "coverage2",
        "coverage2,GRanges-method",
        "coverage2,GRangesList-method",
        "findOverlaps,GRanges,gSet-method",
        "findOverlaps,GRangesList,gSet-method",
        "genomeBuild,GRanges-method",
        "numberProbes",
        "numberProbes,GRanges-method",
        "numberProbes,GRangesList-method",
        "sampleNames,GRanges-method",
        "sampleNames,GRangesList-method",
        "state",
        "state,GRanges-method",
        "state,GRangesList-method"
      ]
    },
    {
      "page": "gSet-class",
      "title": "Container for objects with genomic annotation on SNPs",
      "topics": [
        "checkOrder,gSet-method",
        "db,gSet-method",
        "genomeBuild,gSet-method",
        "genomeBuild<-,gSet,character-method",
        "getArm",
        "getArm,gSet-method",
        "gSet",
        "gSet-class",
        "initialize,gSet-method",
        "makeFeatureGRanges,gSet-method",
        "show,gSet-method"
      ]
    },
    {
      "page": "gSetList-class",
      "title": "Virtual Class for Lists of eSets",
      "topics": [
        "$,gSetList-method",
        "$<-,gSetList-method",
        "annotation,gSetList-method",
        "assayDataList,gSetList-method",
        "chromosome,gSetList-method",
        "coerce,gSetList,list-method",
        "dims,gSetList-method",
        "elementNROWS,gSetList-method",
        "featureDataList,gSetList-method",
        "genomeBuild,gSetList-method",
        "genomeBuild<-,gSetList,character-method",
        "gSetList-class",
        "initialize,gSetList-method",
        "length,gSetList-method",
        "makeFeatureGRanges,gSetList-method",
        "position,gSetList-method",
        "sampleNames,gSetList-method",
        "sampleNames<-,gSetList,character-method",
        "show,gSetList-method",
        "[,gSetList,ANY-method",
        "[,gSetList-method",
        "[[<-,gSetList,ANY,ANY,BafLrrSet-method"
      ]
    },
    {
      "page": "i2p_p2i",
      "title": "Functions to convert probabilities to integers, or integers to probabilities.",
      "topics": [
        "i2p",
        "p2i"
      ]
    },
    {
      "page": "largeObjects",
      "title": "Initialize big matrices/vectors.",
      "topics": [
        "initializeBigArray",
        "initializeBigMatrix",
        "initializeBigVector"
      ]
    },
    {
      "page": "integerMatrix",
      "title": "Coerce numeric matrix (or array) to a matrix (array) of integers, retaining dimnames.",
      "topics": [
        "integerArray",
        "integerMatrix"
      ]
    },
    {
      "page": "is.ffmatrix",
      "title": "Check if object is an ff-matrix object.",
      "topics": [
        "is.ffmatrix"
      ]
    },
    {
      "page": "isPackageLoaded",
      "title": "Check if package is loaded.",
      "topics": [
        "isPackageLoaded"
      ]
    },
    {
      "page": "isSnp-methods",
      "title": "Methods for Function isSnp in package oligoClasses~~",
      "topics": [
        "isSnp",
        "isSnp,character-method",
        "isSnp,GenomeAnnotatedDataFrame-method",
        "isSnp,gSet-method",
        "isSnp,SnpSet-method",
        "isSnp-methods"
      ]
    },
    {
      "page": "kind",
      "title": "Array type",
      "topics": [
        "kind",
        "kind,AffyExonPDInfo-method",
        "kind,AffyExpressionPDInfo-method",
        "kind,AffyGenePDInfo-method",
        "kind,AffyHTAPDInfo-method",
        "kind,AffySNPCNVPDInfo-method",
        "kind,AffySNPPDInfo-method",
        "kind,ExpressionPDInfo-method",
        "kind,FeatureSet-method",
        "kind,GenericPDInfo-method",
        "kind,TilingPDInfo-method"
      ]
    },
    {
      "page": "ldOpts",
      "title": "Set/check large dataset options.",
      "topics": [
        "ldPath",
        "ldSetOptions",
        "ldStatus"
      ]
    },
    {
      "page": "length-methods",
      "title": "Number of samples for FeatureSet-like objects.",
      "topics": [
        "length,FeatureSet-method",
        "length-methods"
      ]
    },
    {
      "page": "library2",
      "title": "Supress package startup messages when loading a library",
      "topics": [
        "library2"
      ]
    },
    {
      "page": "list.celfiles",
      "title": "List CEL files.",
      "topics": [
        "list.celfiles"
      ]
    },
    {
      "page": "ClassesNotExported",
      "title": "eSetList class",
      "topics": [
        "initialize,eSetList-method"
      ]
    },
    {
      "page": "locusLevelData",
      "title": "Basic data elements required for the HMM",
      "topics": [
        "locusLevelData"
      ]
    },
    {
      "page": "makeFeatureGRanges",
      "title": "Construct a GRanges object from several possible feature-level classes",
      "topics": [
        "makeFeatureGRanges"
      ]
    },
    {
      "page": "manufacturer-methods",
      "title": "Manufacturer ID for FeatureSet-like objects.",
      "topics": [
        "manufacturer",
        "manufacturer,DBPDInfo-method",
        "manufacturer,FeatureSet-method",
        "manufacturer-methods"
      ]
    },
    {
      "page": "ocLapply",
      "title": "lapply-like function that parallelizes code when possible.",
      "topics": [
        "ocLapply"
      ]
    },
    {
      "page": "clusterOpts",
      "title": "Cluster and large dataset management utilities.",
      "topics": [
        "ocProbesets",
        "ocSamples"
      ]
    },
    {
      "page": "oligoSetExample",
      "title": "An example instance of oligoSnpSet class",
      "topics": [
        "oligoSet"
      ]
    },
    {
      "page": "oligoSnpSet-methods",
      "title": "Methods for oligoSnpSet class",
      "topics": [
        "baf,oligoSnpSet-method",
        "baf<-,oligoSnpSet-method",
        "calls,oligoSnpSet-method",
        "calls<-,oligoSnpSet,matrix-method",
        "callsConfidence,oligoSnpSet-method",
        "callsConfidence<-,oligoSnpSet,matrix-method",
        "cnConfidence,oligoSnpSet-method",
        "cnConfidence<-,oligoSnpSet,matrix-method",
        "coerce,oligoSnpSet,data.frame-method",
        "copyNumber,oligoSnpSet-method",
        "copyNumber<-,oligoSnpSet,matrix-method",
        "initialize,oligoSnpSet-method",
        "oligoSnpSet-class",
        "position<-,oligoSnpSet,integer-method",
        "updateObject,oligoSnpSet-method"
      ]
    },
    {
      "page": "parStatus",
      "title": "Checks if oligo/crlmm can use parallel resources.",
      "topics": [
        "parStatus"
      ]
    },
    {
      "page": "pdPkgFromBioC",
      "title": "Get packages from BioConductor.",
      "topics": [
        "pdPkgFromBioC"
      ]
    },
    {
      "page": "platform-methods",
      "title": "Platform Information",
      "topics": [
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        "platform,FeatureSet-method",
        "platform-methods"
      ]
    },
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      "page": "pmFragmentLength-methods",
      "title": "Information on Fragment Length",
      "topics": [
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        "pmFragmentLength,AffySNPPDInfo-method",
        "pmFragmentLength-methods"
      ]
    },
    {
      "page": "position-methods",
      "title": "Methods for function position in Package oligoClasses",
      "topics": [
        "position",
        "position,AnnotatedDataFrame-method",
        "position,GenomeAnnotatedDataFrame-method",
        "position,gSet-method",
        "position,SnpSet-method",
        "position-methods"
      ]
    },
    {
      "page": "requireAnnotation",
      "title": "Helper function to load packages.",
      "topics": [
        "requireAnnotation"
      ]
    },
    {
      "page": "requireClusterPkgSetDeprecated",
      "title": "DEPRECATED FUNCTIONS.  Package loaders for clusters.",
      "topics": [
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        "requireClusterPkg-deprecated",
        "requireClusterPkgSet",
        "requireClusterPkgSet-deprecated"
      ]
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    {
      "page": "sampleNames-methods",
      "title": "Sample names for FeatureSet-like objects",
      "topics": [
        "sampleNames,FeatureSet-method",
        "sampleNames-methods"
      ]
    },
    {
      "page": "data-scqsExample",
      "title": "SnpCnvQSet Example",
      "topics": [
        "scqsExample"
      ]
    },
    {
      "page": "clusterOptsDeprecated",
      "title": "DEPRECATED FUNCTIONS.  Cluster and large dataset management utilities.",
      "topics": [
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        "delCluster-deprecated",
        "getCluster",
        "getCluster-deprecated",
        "setCluster",
        "setCluster-deprecated"
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      "page": "data-sfsExample",
      "title": "SnpFeatureSet Example",
      "topics": [
        "sfsExample"
      ]
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      "page": "SnpSet-methods",
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        "confs",
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      "page": "SnpSet2-class",
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      "page": "data-sqsExample",
      "title": "SnpQSet Example",
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      "page": "SummarizedExperiment-methods",
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