Methylation array preprocessing.
This package is downloadable using the following in R:
require(devtools); install_github("metamaden/methyPre")
This package contains a single wrapper function that serves as an all-in-one workflow assembly. It takes an experiment summary object as used in minfi (eg. RGChannelSet, MethylSet, GenomicRatioSet, etc.) and applies minfi normalizations, filters, and batch correction. The workflow decision tree, including all arguments and operations, is as follows:
For more info, see the minfi Bioconductor page. For information on cross-reactive and poor quality probes, see Chen et al 2013 (HM450 platform), and Pidsley et al 2016 (EPIC platform).
Improvements planned: consider contingencies or exceptions and add more messages. Consider adding an estimate for object size and enabling a user interaction (whether to accept or decline based on available memory, the list objects get huge pretty quickly).