somatic-germline

Companion code to the paper:
The context-specific role of germline pathogenicity in tumorigenesis

Code in this repository can be used to recreate the essential parts of the main figures in the manuscript.

Instructions

Install required R packages:

install.packages(c('knitr', 'plyr', 'binom', 'readxl', 'here', 'survival', 'survminer'))

Get supplementary data from manuscript and download germline data from dbGaP.

Place these in the data folder, germline_mutations.maf, and germline_cnvs.txt, or manually enter the file paths in the prerequisites.R script in the scripts directory.

An HTML file containing the figures can be generated from the command-line for each main figure as such:

R -e "rmarkdown::render('scripts/figure-2.Rmd', output_file = 'figure-2.html')"

Install python packges using pip or conda : pandas, numpy, scipt, matplotlib, seaborn

For jupyter notebooks, download notebooks and contents of the data folder. Ensure that the folder structure follows the same relative structure as the GitHub repository and execute notebooks.

Citation

• pending

Contact

E-mail any questions to [email protected], [email protected].