AlleleSet-class         Class "AlleleSet"
CNSet-class             Class "CNSet"
CopyNumberSet-methods   Methods for class CopyNumberSet.
DBPDInfo-class          Class "DBPDInfo"
FeatureSet-class        "FeatureSet" and "FeatureSet" Extensions
SnpSuperSet-class       Class "SnpSuperSet"
addFeatureAnnotation    Add genomic annotation (chromosome, position)
                        for several SNP platforms.
affyPlatforms           Available Affymetrix platforms for SNP arrays
annotationPackages      Annotation Packages
batch                   The batch variable for the samples.
batchStatistics         Accessor for batch statistics uses for copy
                        number estimation and storage of model
                        parameters
calls                   Accessors for Calls and Confidences on a SnpSet
                        object
celfileDate             Cel file dates
checkExists             Checks to see whether an object exists and, if
                        not, executes the appropriate function.
chromosome              Accessors for eSet extensions
chromosome2integer      Converts chromosome to integer
corr                    Methods for class AssayData in the oligoClasses
                        package
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"
ffdf-class              Class "ffdf"
flags                   Batch-level summary of SNP flags.
genomeBuild             Genome Build Information
geometry                Array Geometry Information
getA                    Compute average log-intensities / log-ratios
getBar                  Gets a bar of a given length.
i2p                     Functions to convert probabilities to integers,
                        or integers to probabilities.
initializeBigMatrix     Initialize big matrices/vectors.
is.ffmatrix             Check if object is an ff-matrix object.
isPackageLoaded         Check if package is loaded.
kind                    Array type
ldSetOptions            Set/check large dataset options.
length-methods          Number of samples for FeatureSet-like objects.
list.celfiles           List CEL files.
manufacturer-methods    Manufacturer ID for FeatureSet-like objects.
ocLapply                lapply-like function that parallelizes code
                        when possible.
oligoSnpSet-class       Methods for oligoSnpSet class
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                Accessor to position information
requireAnnotation       Helper function to load packages.
requireClusterPkgSet    Package loaders for clusters.
sampleNames-methods     Sample names for FeatureSet-like objects
scqsExample             SnpCnvQSet Example
setCluster              Cluster and large dataset management utilities.
sfsExample              SnpFeatureSet Example
splitIndicesByLength    Tools to distribute objects across nodes or by
                        length.
sqsExample              SnpQSet Example
