EpigeneticAgePipeline: an R package for comprehensive assessment of epigenetic age metrics from methylation microarrays
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Summary
Epigenetic age is a biological age estimation that is based off nuclear DNA methylation patterns. As an individual ages, methylation sites change in a predictable manner, allowing for the generation of epigenetic age clocks. EpigeneticAgePipeline is an R package that aims to provide a straightforward, out-of-the-box solution for measuring epigenetic age estimates (Horvath, skinHorvath, Hannum, PhenoAge/Levine, GrimAge), as well as two epigenetic age acceleration measures (DunedinPACE, GrimAge Acceleration). Further, EpigeneticAgePipeline imputes cell counts, as well as performs statistical analyses including principal component analysis, normalization, and generation of linear model-based residuals. The pipeline supports Illumina Infinium methylation microarray formats, including HumanMethylation27, HumanMethylation450, and HumanMethylationEPIC. Our package offers an all-in-one solution to generate epigenetic age estimates from input IDAT files or preprocessed methylation beta values.
Availability
EpigeneticAgePipeline is implemented in R (3.5 or greater) and available on GitHub at https://github.com/CastellaniLab/EpigeneticAgePipeline
Supplementary Information
PDF file submitted along with manuscript.
