This package provides manifest for Illumina methylation EPIC array v2.0. The data is based on the file https://support.illumina.com/content/dam/illumina-support/documents/downloads/productfiles/methylationepic/MethylationEPIC%20v2%20Files.zip from https://support.illumina.com/array/array_kits/infinium-methylationepic-beadchip-kit/downloads.html.
A script for creating the data object in this package is in system.files("scripts", "manifest.R", package = "IlluminaHumanMethylationEPICv2manifest"), which is slightly adjusted from the original script in the IlluminaHumanMethylationEPICmanifest package.
When using with the minfi package, you can manually set the “array” element by providing the prefix (removing the string “manifest”):
RGset = read.metharray.exp(...)
annotation(RGset)["array"] = "IlluminaHumanMethylationEPICv2"
# explained in the IlluminaHumanMethylationEPICv2anno.20a1.hg38 package
annotation(RGset)["annotation"] = "20a1.hg38"
BiocManager::install("jokergoo/IlluminaHumanMethylationEPICv2manifest")
# or
remotes::install_github("jokergoo/IlluminaHumanMethylationEPICv2manifest")