methylumi (version 2.18.2)

MethyLumiM-class: Class "MethyLumiM": for Illumina Methylation microarray data using logRatios

Description

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.

Objects from the Class

Objects can be created by calls of the form new("MethyLumiM", exprs, methylated, unmethylated, detection, methylated.N, unmethylated.N, ..., assayData). The "exprs" is a matrix of M-values, which is the log2 ratio of methylated and unmethylated probe intensities; "methylated" and "unmethylated" are intensity matrix measured by methylated and unmethylalted probes of Illumina Infinium methylation microarray; "detection" is the detection p-value outputted by Illumina GenomeStudio software; "methylated.N" and "unmethylated.N" are bead numbers for methylated and unmethylalted probes. "exprs", "methylated" and "unmethylated" information are required for MethyLumiM class. When creating a new MethyLumiM object, the information of "exprs", "methylated", "unmethylated" and "detection" can also be provided directly through "assayData".

Extends

Class "ExpressionSet", directly. Class "eSet", by class "ExpressionSet", distance 2. Class "VersionedBiobase", by class "ExpressionSet", distance 3. Class "Versioned", by class "ExpressionSet", distance 4.

References

1. Du, P., Zhang, X, Huang, C.C., Jafari, N., Kibbe, W.A., Hou, L., and Lin, S.M., (2010) 'Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis'

See Also

MethyLumi-class and MethyLumiSet-class

Examples

showClass("MethyLumiM")