Scripts accompanying "Blood- and brain-based epigenome-wide association studies of smoking" paper.
Five folders containing annotated scripts to perform the following five main analyses described in the manuscript:
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EWAS of pack years of smoking (BayesR)
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High resolution EWAS (TWIST)
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Predictor of pack years of smoking (EpiScore)
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Brain-based EWAS of smoking (Brain)
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GWAS of pack years of smoking (GWAS)
Additionally, the repository contains a demo package.
- Demo/replication package with a small simulated dataset to demonstrate the code (Replication)
Demo package can be executed on a standard computer. It was tested on a following machine:
RAM: 16 GB CPU: 4 cores @ 2.6GHz OS: Windows
Other scripts were executed on a high performance computing cluster with no "non-standard" hardware. It is not advisable to run them on a local machine ("normal" computer). The following specs are advisable for optimal performance:
RAM: 256 GB CPU: 32 cores @ 2.7GHz OS: Linux
All code is written in R (version 4.3.1) or python (version 3.9.7). Packages used and versions detailed in manuscript. In addition, BayesR+ version 0.1.0 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7280277/) and LDSC version 1.0.1 was used.
Demo package: Please install R. The demo package scripts contain installation commands, which should take care of any missing libraries. Typical install and run time on a "normal" computer is less than 15 minutes.
Other scripts: Please follow installation instructions of BayesR+ (https://github.com/ctggroup/BayesRRcmd/blob/master/README.md, version 0.1.0), Genome-wide Complex Trait Analysis (GCTA) version 1.93.2 Linux (https://yanglab.westlake.edu.cn/software/gcta/) and LDSC, version 1.0.1 (https://github.com/bulik/ldsc).
To run the demo, please go to Replication/scripts/ and execute the scripts in order dictated by their names. Further instructions are available in Replication/How_to_run_the_demo.docx.
MIT License
Copyright (c) 2024 Aleksandra Daria Chybowska
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
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