methylumi-package: Handle Illumina methylation data
In methylumi: Handle Illumina methylation data

Description Details Author(s) References See Also

This package contains a class structure for handling methylation data from Illumina as well as utility functions for loading the data from files generated by Illumina. Normalization that attempts to correct for dye bias is also included.

Important data classes include: MethyLumiSet and MethyLumiQC, both of which are subsets of the MethyLumi class, which is a subset of the eSet class.

A worked example of the use of the package can be found by typing: openVignette().

A full listing of the available documentation can be obtained by typing help.start() and selecting methylumi from the Packages link or by typing library(help="methylumi").

If you use the methylumIDAT function or its out-of-band preprocessing mechanisms in your work, a citation to the paper "Low-level processing of Illumina Infinium DNA methylation beadarrays" by TJ Triche, DJ Weisenberger, D Van Den Berg, KD Siegmund, and PW Laird, Nucleic acids research, 2013, would be appreciated.