EPICv2_DNAm_QC_preprocessing.Rmd comprises of the steps involved in quality check (QC), normalization and preprocessing of DNA methylation data obtained from the EPICv2 array.
Please cite: Zhuang BC, Jude MS, Konwar C, et al. Discrepancies in readouts between Infinium MethylationEPIC v2.0 and v1.0 reflected in DNA methylation-based tools: implications and considerations for human population epigenetic studies Available from: https://www.biorxiv.org/content/10.1101/2024.07.02.600461v2
Additional QC steps for both EPICv2 and EPICv1 were performed as described in Konwar C, Asiimwe R, Inkster AM, Merrill SM, Negri GL, Aristizabal MJ, et al. Risk-focused differences in molecular processes implicated in SARS-CoV-2 infection: corollaries in DNA methylation and gene expression. Epigenetics Chromatin. 2021;14:54.(https://github.com/kobor-lab/Public-Scripts/blob/master/COVID-19/DNAme%20preprocessing.Rmd)