/BCAA-BP-MR

R code to reproduce Mendelian randomization analyses evaluating the relationship between branch-chain amino acids and blood pressure

Primary LanguageHTMLMIT LicenseMIT

Circulating Branch-Chain Amino Acids and Blood Pressure: A Mendelian Randomization Study

DOI

This repository contains R code to reproduce Mendelian randomization analyses evaluating the relationship between branch-chain amino acids and blood pressure. The results of these analyses are published as part of:

Murashige et. al. (2022). Extra-cardiac BCAA catabolism lowers blood pressure and protects from heart failure.

Usage

The following steps should allow the user to reproduce the BCAA-BP-MR.html document, which contains additional description of the data sources, methods, and rendered plots/tables/results:

  1. Clone/download the contents of this repository into a new directory.
  2. Open BCAA-BP-MR.qmd in RStudio and/or render the document using Quarto. This file is a Quarto markdown document, including code and text which when rendered reproduce the BCAA-BP-MR.html document.

Notes

  • All required R package dependencies have been captured by the renv package (https://rstudio.github.io/renv/index.html), and are stored in renv.lock. All required packages will be automatically installed using the renv::restore() function when the document is rendered.
  • Summary genetic data used to construct genetic instruments for branch chain amino acids and the corresponding effects on blood pressure traits will be queried from the IEU OpenGWAS Project, or downloaded from the Pan-UK Biobank project into the Data/ directory. These files are large (~2GB each), and are therefore not included in the repository directly.
  • The Data/ directory contains additional information needed to test for enrichment of BCAA-associated genetic variants with genes known to be involved in BCAA metabolism (additional details described in BCAA-BP-MR.qmd).
  • Where possible the document reads from cached results located in the BCAA-BP-MR_cache/ and BCAA-BP-MR_files/ directories to speed up rendering. To render the document entirely from scratch, change cache: true to cache: false in the YAML header of BCAA-BP-MR.qmd.

System Requirements

  • RAM: 32GB (recommended when rendering from scratch, as GWAS summary statistics from Pan-UK Biobank are large; memory requirement should be lower when rendering from cached output or excluding Pan UK Biobank analyses)