Analysis for Miller et al. 2022

Purpose: The purpose of this repo is to enable replication of the figures and analyses from the Miller et al., 2022 manuscript. The published version of the manuscript is found here.

Quick-start

To re-create the figures from the manuscript, do the following:

1. Clone the repo

git clone https://github.com/Bishop-Laboratory/RLoop-QC-Meta-Analysis-Miller-2022.git
cd RLoop-QC-Meta-Analysis-Miller-2022/

2. System dependencies

There are some system dependencies which must be installed for compiling some packages. For Windows, this requires RTools.

To aid in the discovery of system requirements, use getsysreqs.

Install getsysreqs:

R -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")'
R -e 'remotes::install_github("mdneuzerling/getsysreqs", force=TRUE)'

Capture dependencies (replace with your OS/Version):

OS="ubuntu"
VER="20.04"
REQS=$(Rscript -e 'options(warn = -1); cat(getsysreqs::get_sysreqs("renv.lock", distribution = "'$OS'", release = "'$VER'"))' | sed s/"WARNING: ignoring environment value of R_HOME"//)

Install (Ubuntu):

sudo apt install $REQS -y

2. Python dependencies

Install python (only tested on v3.8). Then restore from requirements.

python -m venv venv
source venv/bin/activate
pip install -r requirements.txt

3. Restore the renv

R -e 'if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")'
R -e 'renv::restore()'

4. Run the script

Rscript figures.R

Troubleshooting

If any issues arise or anything is unclear, please submit an issue.