AlleleSet-class         Class "AlleleSet"
AssayDataList           Create a list of assay data elements
BeadStudioSet-class     Class '"BeadStudioSet"'
BeadStudioSetList-class
                        BeadStudioSetList class
CNSet-class             Class "CNSet"
CopyNumberSet-class     Class '"CopyNumberSet"'
CopyNumberSet-methods   Methods for class CopyNumberSet.
DBPDInfo-class          Class "DBPDInfo"
FeatureSet-class        "FeatureSet" and "FeatureSet" Extensions
GenomeAnnotatedDataFrame-class
                        Class '"GenomeAnnotatedDataFrame"'
GenomeAnnotatedDataFrameFrom
                        Methods for Function
                        GenomeAnnotatedDataFrameFrom in Package
                        oligoClasses
RangedDataCBS           Utility functions for RangedData extensions for
                        storing ranged data on copy number variants.
RangedDataCopyNumber-class
                        Classes in MinimumDistance for data on ranges
SnpSet2-class           Class '"SnpSet2"'
SnpSuperSet-class       Class "SnpSuperSet"
affyPlatforms           Available Affymetrix platforms for SNP arrays
annotationPackages      Annotation Packages
baf                     Miscellaneous generics.  Methods defined in
                        packages that depend on oligoClasses
batch                   The batch variable for the samples.
batchStatistics         Accessor for batch statistics uses for copy
                        number estimation and storage of model
                        parameters
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
corr                    Methods for class AssayData in the oligoClasses
                        package
coverage2,GRanges-method
                        Methods for GRanges objects
createFF                Create ff objects.
db                      Get the connection to the SQLite Database
efsExample              ExpressionFeatureSet Object
exprs-methods           Accessor for the 'exprs' slot
ff_matrix-class         Class "ff_matrix"
ff_or_matrix-class      Class '"ff_or_matrix"'
ffdf-class              Class "ffdf"
findOverlaps            Find markers that overlap with a query set of
                        ranges
flags                   Batch-level summary of SNP flags.
gSet-class              Container for objects with genomic annotation
                        on SNPs
gSetList-class          Virtual Class for Lists of eSets
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
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
splitIndicesByLength    Tools to distribute objects across nodes or by
                        length.
sqsExample              SnpQSet Example
