# Scripts and deposited data

This directory contains R and python scripts along with the data necessary to

generate the results described in the manuscript: 'cholesteryl ester transfer

protein (CETP) as a drug target for cardiovascular disease'.

## Directory content

.

├── README.md

├── scripts

├── figures

├── MR_data

├── TRIAL_data

└── PICKLED_data

The `scripts` directory contains the computer codes necessary to

generate the figures which get saved to the `figures` directory.

The scripts source data from the `MR_data` and `TRIAL_data` directories.

The `PICKLED_data` directory contains the python pickled files from

which we extracted the .csv files in `MR_data` -- these files can be ignored.

## Computer scripts

The directory root contains various R (.R) and python (.py) scripts that

will process the data files.

It also contains a `cetp_conda_env.yml` file to conda install the

necessary R and python modules:

```

cd scripts

conda env create -f cetp_conda_env.yml

```

This creates the `cetp` conda environment.

To generate the figures, please run the following `bash` script:

```

# run from the scripts directory

./run_scripts.sh

```

### Input and output

* scripts/MR_heatmap.py

: Takes the MR_data .tsv files and returns Figures 2 and 5.

* scripts/MR_metabolites.R

: Takes the MR_data .tsv/csv files and returns Figure 4.

* scripts/MR_forestplots.R

: Takes the MR_data .tsv files and returns Figure 3.

* scripts/RCT_forestplots.R

: Takes the TRIAL_data .xlsx files and returns Figure 1.

## Contact

Please contact Floriaan Schmidt for any queries: amand.schmidt@ucl.ac.uk .