BIOCLOCK

This repository contains the code used for the BIOCLOCK pilot study. The manuscript is currently being prepared for submission and will be available soon.

Scripts

This repository contains three main scripts:

• 1_preprocessing.R: This script performs quality control on the DNA methylation data, applies the 101 preprocessing pipelines, and estimates the epigenetic ages and blood leukocyte composition.
• 2_analysis.R: This script contains the statistical analyses perfomed on the epigenetic ages and other phenotypic variables.
• 3_figures.R: This script contains the code used to generate the figures in the manuscript.

It also contains three addtitional scripts:

• function_runPipelines.R: This script is used to run the 101 preprocessing pipelines and is adapted from this repository: https://github.com/anilpsori/_pipelines_and_biomarkers/tree/main.
• Biolearn_EpiAge.py: This script is used to calculate GrimAge epigenetic age using the Biolearn python package (https://github.com/bio-learn/biolearn).
• runcalcPCClock.R: This script is used to calculate epigenetic age according to the principal component clocks and is adapted from this repository: https://github.com/MorganLevineLab/PC-Clocks.

Directory structure

The scripts rely on the following directory structure:

.
├── Data
│   ├── Infinium
│   ├── Objects
│   └── Pheno
├── Images
│   ├── Paper
│   ├── PrePro
│   └── QC
├── PC_Clocks
├── Results
│   ├── Analysis
│   └── PrePro
└── Scripts
    └── Additional

Environment Information

For reproducibility, see the full R session info in Environment.md.