beta2clocks

Docker container for calculating epigenetic clocks from DNA methylation data using methylCIPHER.

Quick Start

docker pull ghcr.io/higginschenlab/beta2clocks:latest

Usage

Place your _cleaned.RData file in any local directory, then run:

docker run --rm \
  -v /path/to/your/data:/home/data:rw \
  ghcr.io/higginschenlab/beta2clocks:latest \
  Rscript pipeline/entrypoint.R --input data/YourDataset_cleaned.RData

Remember to set /path/to/your/data to the directory containing your file — that's the only thing to change.

Results are saved alongside the input file in the same directory.

Input Format

An .RData file containing:

• A variable starting with DNAm — beta matrix (samples as rows, CpGs as columns)
• A variable starting with pheno — phenotype data with age and sex columns. Expected column names are cAGE and cFEMALE.

Options

Batch Size

Use --batch-size N to control how many samples are processed at once (default: 250, set to 0 to disable batching):

Rscript pipeline/entrypoint.R --input data/YourDataset_cleaned.RData --batch-size 100

Running Specific Clocks

Use --clocks with a comma-separated list to run only specific clocks:

Rscript pipeline/entrypoint.R --input data/YourDataset_cleaned.RData --clocks Hannum,PhenoAge,DunedinPACE

Clock names match the calc{Name}() function names from methylCIPHER. WhatSex and Zhang2019 always run as they are dependencies for downstream clocks.

Clocks Included

WhatSex, Zhang2019, Hannum, Horvath1, Horvath2, PhenoAge, DNAmTL, CausAge, AdaptAge, DamAge, GrimAgeV1, GrimAgeV2, PCClocks, SystemsAge, DunedinPACE, DunedinPoAm38, StochasticClocks, EpiDish, eFRS, DNAmIC

Citation

To-do

License

To-do