Objective

To study the mutational and adaptive landscape of lung adenocarcinoma (LUAD) and how it is altered by the mutagenic and physiological effects of tobacco smoking using an aggregated dataset of LUAD genomes.

Requirements

• Python, ideally installed with pyenv (https://github.com/pyenv/pyenv) to be able to have exactly the same version (3.9.5) as the tested, but otherwise at least 3.7 so that the order of dictionaries is preserved.
• R (at least version 4.0; in debian or ubuntu install the packages r-base and r-base-dev)
• the development files for libcurl (OpenSSL flavour) are required for many R packages including RCurl (that is required for cancereffectsizeR). In debian or ubuntu install the libcurl4-openssl-dev package

Installation

To install this repository, clone it with

git clone https://github.com/Townsend-Lab-Yale/lung-smoking.git

or if the Github CLI tool is installed,

gh repo clone Townsend-Lab-Yale/lung-smoking

Expected time: a few seconds

Setup

To prepare the system for running the analysis, within the code directory run

./setup.sh

and follow the instructions.

Expected time: a few minutes

Demo

To run a short demo to confirm correct setup of the software, within the code directory run

cd variants
Rscript demo.R
cd ../
source .venv/bin/activate
python demo.py

Expected time: around twenty minutes

Analysis

To run the analysis, within the code directory run

cd variants
Rscript main.R
cd ../
source .venv/bin/activate
python main.py

Results can be analyzed using the Jupyter notebooks provided in the result_analysis directory.

To obtain the gene expression results, run through the Jupyter notebook differential_expression.ipynb in the code directory.

Expected time: a few hours