MethyLumiM-class
(Package: methylumi) :
Class "MethyLumiM": for Illumina Methylation microarray data
MethyLumiM is a class inherited from ExpressionSet-class. It is designed for Illumina Methylation microarray data. The exprs dataMatrix included in the assayData slot of MethyLumiM object includes a matrix of M-values, which is the log2 ratio of methylated and unmethylated probe intensities. The MethyLumiM class include a boxplot function uniquely designed for two-mode histogram data. It also include a coerce function to map from MethyLumi-class, MethyLumiSet-class or other eSet-class inherited object to MethyLumiM class object.
This class inherits from the MethyLumi class (and therefore, from eSet in Biobase) and is designed to hold QC data from Illumina Beadstudio output. These data can be potentially useful when determining the cause for quality problems.
This class inherits from the MethyLumi class (and therefore, from eSet in Biobase) and is designed to hold both the intensities and the calculated betas, as well as pvalues if present.
The sentrix IDs from an illumina sentrix array contain positional information that might be useful. This function simply extracts that information from the ID itself.
featureFilter
(Package: methylumi) :
Annotation-based Filtering of Features (CpG sites) in a
Features with insufficient annotation carry little value for the subsequent data analysis. The function featureFilter provides options of filtering features (CpG sites) from a MethyLumiSet (or MethyLumiM) object based on available annotation data.
The Illumina methylation platforms use two distinct platforms, the "goldengate" platform and the "infinium" platform. Each of these uses different file formats as well as different assay techologies. To make the downstream data handling more straightforward and uniform between the two different systems, a simple mapping from the column names in the output files from the Illumina software is used to convert things from Red/Green or Cy5/Cy3 to unmethylated/methylated. This function simply returns that mapping.
providing 
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