affyPlatforms           Available Affymetrix platforms for SNP arrays
AlleleSet-class         Class "AlleleSet"
annotationPackages      Annotation Packages
AssayDataList           Create a list of assay data elements
assayDataList-methods   Accessor for slot assayDataList in Package
                        'oligoClasses'
baf                     Miscellaneous generics.  Methods defined in
                        packages that depend on oligoClasses
baf,RangedSummarizedExperiment-method
                        Methods for RangedSummarizedExperiment objects
batch                   The batch variable for the samples.
batchStatistics         Accessor for batch statistics uses for copy
                        number estimation and storage of model
                        parameters
BeadStudioSet-class     Class '"BeadStudioSet"'
BeadStudioSetList-class
                        List classes with assay data listed by
                        chromosome
calls                   Accessors and methods for SnpSet objects
celfileDate             Cel file dates
celfileName             Extracts complete cel file name from a CNSet
                        object
checkExists             Checks to see whether an object exists and, if
                        not, executes the appropriate function.
checkOrder              Checks whether a eSet-derived class is ordered
                        by chromosome and physical position
chromosome-methods      Methods for function chromosome in package
                        oligoClasses
chromosome2integer      Converts chromosome to integer
CNSet-class             Class "CNSet"
CopyNumberSet-class     Class '"CopyNumberSet"'
CopyNumberSet-methods   Methods for class CopyNumberSet.
corr                    Methods for class AssayData in the oligoClasses
                        package
createFF                Create ff objects.
db                      Get the connection to the SQLite Database
DBPDInfo-class          Class "DBPDInfo"
efsExample              ExpressionFeatureSet Object
exprs-methods           Accessor for the 'exprs' slot
featureDataList-methods
                        Accessor for slot 'featureDataList' in Package
                        'oligoClasses' ~~
FeatureSet-class        "FeatureSet" and "FeatureSet" Extensions
ff_matrix-class         Class "ff_matrix"
ff_or_matrix-class      Class '"ff_or_matrix"'
ffdf-class              Class "ffdf"
flags                   Batch-level summary of SNP flags.
GenomeAnnotatedDataFrame-class
                        Class '"GenomeAnnotatedDataFrame"'
GenomeAnnotatedDataFrameFrom
                        Methods for Function
                        GenomeAnnotatedDataFrameFrom in Package
                        oligoClasses
genomeBuild             Genome Build Information
geometry                Array Geometry Information
getA                    Compute average log-intensities / log-ratios
getBar                  Gets a bar of a given length.
getSequenceLengths      Load chromosome sequence lengths for UCSC
                        genome build hg18 or hg19
gSet-class              Container for objects with genomic annotation
                        on SNPs
gSetList-class          Virtual Class for Lists of eSets
i2p                     Functions to convert probabilities to integers,
                        or integers to probabilities.
initialize,eSetList-method
                        eSetList class
initializeBigMatrix     Initialize big matrices/vectors.
integerMatrix           Coerce numeric matrix (or array) to a matrix
                        (array) of integers, retaining dimnames.
is.ffmatrix             Check if object is an ff-matrix object.
isPackageLoaded         Check if package is loaded.
isSnp-methods           Methods for Function isSnp in package
                        oligoClasses~~
kind                    Array type
ldSetOptions            Set/check large dataset options.
length-methods          Number of samples for FeatureSet-like objects.
library2                Supress package startup messages when loading a
                        library
list.celfiles           List CEL files.
locusLevelData          Basic data elements required for the HMM
makeFeatureGRanges      Construct a GRanges object from several
                        possible feature-level classes
manufacturer-methods    Manufacturer ID for FeatureSet-like objects.
ocLapply                lapply-like function that parallelizes code
                        when possible.
ocSamples               Cluster and large dataset management utilities.
oligoSet                An example instance of oligoSnpSet class
oligoSnpSet-class       Methods for oligoSnpSet class
open                    Open and close methods for matrices and numeric
                        vectors
parStatus               Checks if oligo/crlmm can use parallel
                        resources.
pdPkgFromBioC           Get packages from BioConductor.
platform-methods        Platform Information
pmFragmentLength-methods
                        Information on Fragment Length
position-methods        Methods for function position in Package
                        oligoClasses
requireAnnotation       Helper function to load packages.
requireClusterPkgSet    DEPRECATED FUNCTIONS.  Package loaders for
                        clusters.
sampleNames-methods     Sample names for FeatureSet-like objects
scqsExample             SnpCnvQSet Example
setCluster              DEPRECATED FUNCTIONS.  Cluster and large
                        dataset management utilities.
sfsExample              SnpFeatureSet Example
SnpSet2-class           Class '"SnpSet2"'
SnpSuperSet-class       Class "SnpSuperSet"
splitIndicesByLength    Tools to distribute objects across nodes or by
                        length.
sqsExample              SnpQSet Example
state                   Methods for GRanges objects
