Companion code to the paper:
Tumour lineage shapes BRCA-mediated phenotypes
Code in this repository can be used to recreate the essential parts of the main figures in the manuscript. All code is in R.
Install required R packages:
install.packages(c('knitr', 'plyr', 'tidyverse', 'patchwork', 'binom', 'ggrepel', 'grid', 'readxl', 'ggbeeswarm', 'here', 'survival', 'survminer'))Get supplementary data from manuscript and download germline data from dbGaP.
Place these in the data folder, with the names Taylor_SItables.xlsx, germline_mutations.maf, and germline_cnvs.txt, or manually enter the file paths in the prerequisites.R script in the r directory.
An HTML file containing the figures can be generated from the command-line for each main figure as such:
R -e "rmarkdown::render('r/figure-1.Rmd', output_file = 'figure-1.html')"- URL: https://www.nature.com/articles/s41586-019-1382-1
- DOI: 10.1038/s41586-019-1382-1
E-mail any questions to [email protected].