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# Baboon Epigenetic Aging (Anderson and Johnston et al. 2021, _eLife_)

This repository holds the code used to analyze the data from, and recreate the results in, _Anderson and Johnston et al. 2021_ (https://doi.org/10.7554/eLife.66128). These scripts include:

  (i) Scripts for trimming, mapping, and filtering reduced-representation bisulfite sequencing data (Trim_map_filter).  
  
  (ii) Parallelizable scripts for normalizing methylation ratios and building elastic net models through leave-one-out internal cross-validation (Elastic_net_model).  
  
  (iii) Linear modeling of age predictions (Linear_modeling).  
  
  (iv) Enrichment analysis of clock sites (Enrichment_analyses).  


We also include simulations related to a comment that came up during review regarding the importance of controlling for age structure in predicted epigenetic ages (Simulations_for_reviewers).