CpGs                    Data frame describing loci on the 27 and 450k
                        arrays.
IDATsToMatrices         convert multiple idats to matrices
IDATtoMatrix            process a single IDAT (just the mean
                        intensities)
MethyLumi-class         The base class for storing Illumina Methylation
                        data
MethyLumiM-class        Class "MethyLumiM": for Illumina Methylation
                        microarray data using logRatios
MethyLumiQC-class       Class '"MethyLumiQC"' for holding Illumina
                        methylation QC data
MethyLumiSet-class      Class '"MethyLumiSet"' for containing Illumina
                        methylation data
betas                   methylumi accessors
combine27k450k          Generics defined in methylumi
estimateM               Estimate methylation M-value matrix
extractBarcodeAndPosition
                        Extract the Barcode and Position Information
                        from Sentrix ID
featureFilter           Annotation-based Filtering of Features (CpG
                        sites) in a MethyLumiSet or MethyLumiM object
getAssayDataNameSubstitutions
                        Return a data.frame of AssayData name
                        substitutions.
methylData-class        Class '"methylData"', superclass for
                        MethyLumiSet and MethyLumiM
methylumIDAT            methylumIDAT
methylumi-package       Handle Illumina methylation data
methylumiR              Load data from Illumina methylation platform
mldat                   Example SAM format Illumina methylation dataset
normalizeMethyLumiSet   Normalize a MethyLumiSet, accounting for dye
                        bias
plotSampleIntensities   Plot the sample intensities.
qcplot                  Methods for dealing with control data for
                        Illumina methylation data.
stripOOB                Strip excessive probe-level data from
                        MethyLumiSets
tcgaPipeline            Total convenience function for processing IDATs
                        like tcga
varFilter               Variation-based Filtering of Features (CpG
                        sites) in a MethyLumiSet or MethyLumiM object
