Illumina Human Methylation Manifest based on 1.0 B5 to be used with R and minfi.
The default Manifest used by minfi comes from the bioconductor package IlluminaHumanMethylationEPICmanifest which at it's current version 0.6.0 uses manifest 1.0 B2.
This package provides a manifest based on the 1.0B5 manifest file infinium-methylationepic-v-1-0-b5-manifest-file-csv.zip from Illumina.
You can install it along with the 1.0B5 annotation in R by using the devtools library and doing:
library(devtools)
install_github("achilleasNP/IlluminaHumanMethylationEPICmanifest")
install_github("achilleasNP/IlluminaHumanMethylationEPICanno.ilm10b5.hg38")and force minfi to use the package by setting the annotation of your "RGChannelSet" object as below:
RGset@annotation = c(array = "IlluminaHumanMethylationEPIC", annotation = "ilm10b5.hg38")