missMethyl is a library for the analysis of Illumina's 450K human methylation BeadChip. Specifically, functions for SWAN normalisation and differential variability analysis are provided. SWAN normalisation uses probe specific information, and the differential variability procedure uses linear models which can handle any designed experiment.
Normalisation of the 450K arrays can be performed using the function
Differential variability analysis can be performed by calling
varFit followed by
topVar for a list of the top ranked differentially variable CpGs between conditions.
More detailed help documentation is provided in each function's help page.
Belinda Phipson and Jovana Maksimovic
Maintainer: Belinda Phipson <firstname.lastname@example.org>, Jovana Maksimovic <email@example.com>
Maksimovic, J., Gordon, L., Oshlack, A. (2012). SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips. Genome Biology, 13:R44.
Phipson, B., and Oshlack, A. (2014). DiffVar: A new method for detecting differential variability with application to methylation in cancer and aging. Genome Biology, 15:465.