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.
Details
Important data classes include: [MethyLumiSet-class] and [MethyLumiQC-class], both of which are subsets of the [MethyLumi-class] 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.
| Package: | methylumi |
| Type: | Package |
| License: | GPL |