PheEWAS sex differences

Analysis on sex differences in NHANES dataset. The analysis plan is here.

Clone repository

To clone the repository, on your terminal type:

git clone https://github.com/tomszar/PheEWAS_sexdiff.git

Then, enter the repository and follow the next instructions

cd PheEWAS_sexdiff

Environment setup

The repository provides an environment.yml file to use with conda.

First, install anaconda on your local computer or user server account following the appropriate directions. Next, on the terminal, in the root of this repository, install the conda environment by running:

conda env create -f environment.yml

If the installation fails, you can install the environment manually, by running the following:

conda create --name py_clarite python<=3.9 jupyterlab matplotlib networkx numpy nxviz pandas pip rpy2 scikit-learn scipy statsmodels
conda activate py_clarite
pip install clarite

Data

• The NHANES datasets were obtained from already unified dataset by Patel et al 2016. The data is stored in Dryad

Replicate the analysis

To replicate the analysis, two bash scripts are provided; one is intended to run on a server, run_server.sh, while the other is intended to run on a local computer run_local.sh.

On a server

On your server terminal, type

qsub run_server.sh

The parameters used in the script are the ones used in the Penn State Roar server. Depending on the system you will need to modify, remove, or add parameters to the script. The script also contains the creation and activation of the conda environment; you can alternatively make sure to install the environment before running the bash script and comment those lines.

On a local computer

On the terminal type:

conda activate py_clarite
bash run_local.sh > run_local.log