methscore: a comprehensive R function for DNA methylation-based health predictors

Author:

Xu Zongli1ORCID,Niu Liang2ORCID,Kresovich Jacob K3,Taylor Jack A4

Affiliation:

1. Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences , Research Triangle Park, NC, 27709, United States

2. Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati , Cincinnati, OH, 45267, United States

3. Departments of Cancer Epidemiology & Breast Oncology, H. Lee Moffitt Cancer Center & Research Institute , Tampa, FL, 33612, United States

4. Epidemiology Branch, National Institute of Environmental Health Sciences , Research Triangle Park, NC, 27709, United States

Abstract

Abstract Motivation DNA methylation-based predictors of various biological metrics have been widely published and are becoming valuable tools in epidemiologic studies of epigenetics and personalized medicine. However, generating these predictors from original source software and web servers is complex and time consuming. Furthermore, different predictors were often derived based on data from different types of arrays, where array differences and batch effects can make predictors difficult to compare across studies. Results We integrate these published methods into a single R function to produce 158 previously published predictors for chronological age, biological age, exposures, lifestyle traits and serum protein levels using both classical and principal component-based methods. To mitigate batch and array differences, we also provide a modified RCP method (ref-RCP) that normalize input DNA methylation data to reference data prior to estimation. Evaluations in real datasets show that this approach improves estimate precision and comparability across studies. Availability and implementation The function was included in software package ENmix, and is freely available from Bioconductor website (https://www.bioconductor.org/packages/release/bioc/html/ENmix.html).

Funder

National Institute of Environmental Health Sciences

Publisher

Oxford University Press (OUP)

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