BeatAML2 Manuscript Workflow

Setup

Clone into beataml2_manuscript directory

Data

The beataml2_manuscript/data directory should contain the following files:

van Galen et al 2019 Table S3

• 1-s2.0-S0092867419300947-mmc3.xlsx

Can be retrieved by downloading from the BeatAML2 page

• beataml_waves1to4_norm_exp_dbgap.txt
• beataml_probit_curve_fits_v4_dbgap.txt
• beataml_wes_wv1to4_mutations_dbgap.txt
• beataml_drug_families.xlsx
• beataml_wv1to4_clinical.xlsx
• wgcna/merged_older_wgcna_kme.RData

To run

cd beataml2_manuscript

R
renv::restore()
#note it mentions repair of dependency tree, seems to be an renv issue with packages not directly used
targets::tar_make()

Note: To reproduce fully, need to use R-4.03

To isolate this procedure from your system's R, use of Docker is recommended.

Docker instructions

Use of the no_font branch is recommended as the specification of Arial font family can cause issues in Ubuntu

cd beataml2_manuscript
git checkout no_font
cd ..

docker pull r-base:4.0.3

docker run -it -w /data/beataml2_manuscript -v $PWD:/data r-base:4.0.3 /bin/bash

apt-get -y update
apt-get -y  install libcairo2-dev libxt-dev libxml2-dev libssl-dev libcurl4-openssl-dev

mkdir figures
mkdir output_files

$ R

renv::restore()
targets::tar_make()