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, B. C., Jude, M. S., Konwar, C., Yusupov, N., Ryan, C. P., Engelbrecht, H. R., ... & Kobor, M. S. (2025). Accounting for differences between Infinium MethylationEPIC v2 and v1 in DNA methylation–based tools. Life science alliance, 8(9). (https://www.life-science-alliance.org/content/8/9/e202403155)
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)