betas                   methylumi accessors
combine27k450k          Generics defined in methylumi
CpGs                    Data frame describing loci on the 27 and 450k
                        arrays
estimateM               Estimate methylation M-value matrix
extractBarcodeAndPosition
                        Extract the barcode and position information
                        from a 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
IDATsToMatrices         convert multiple idats to matrices
IDATtoMatrix            process a single IDAT (just the mean
                        intensities)
methylData-class        Class '"methylData"', superclass for
                        MethyLumiSet and MethyLumiM
MethyLumi-class         The base class for storing Illumina Methylation
                        data
methylumi-package       Handle Illumina methylation data
MethyLumi-strippers     Strip excessive probe-level data from
                        MethyLumiSets
methylumIDAT            methylumIDAT
MethyLumiM-class        Class "MethyLumiM": for Illumina Methylation
                        microarray data using logRatios
MethyLumiQC-class       Class '"MethyLumiQC"' for holding Illumina
                        methylation QC data
methylumiR              Load data from an Illumina methylation platform
MethyLumiSet-class      Class '"MethyLumiSet"' for containing Illumina
                        methylation data
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
tcgaPipeline            Total convenience function for processing IDATs
                        like tcga
varFilter               Variation-based filtering of features (CpG
                        sites) in a MethyLumiSet or MethyLumiM object
