This repository contains analyses performed for the accompanying article, and were originally written and performed using R 4.1.1. The analysis is separated into several files, all sourcing a file with the environment and accessory functions. Each should be run sequentially. A separate folder contains necessary supplemental data files.
To recreate analyses, clone this repo and work from the analysis directory. Before performing QTL mapping, you will need to create a genome cache using the code within analysis/3a_genome_cache.R -- this is sourced when running the mapping code. Retrieve Collaborative Cross MRCAs for all strains included in the study and MegaMUGA reference clusters and adjust paths in code accordingly.
This analysis is open source under an MIT license.