Maternal Cardiovascular-Related Single Nucleotide Polymorphisms, Genes and Pathways Associated with Early-Onset Preeclampsia

This repository holds the code for the paper.

You can find more information and data on the OSF project page: https://osf.io/ecpw6/

Results

The paper (todo: add link to paper) contains a summary and explanation of the findings.

The src folder contains the scripts used to do the analysis.

You can also skim the R exploratory analysis of the data, without running it yourself, in notebook format here: https://breckuh.github.io/eopegwas/src/main.nb.html

Results of snpQC report are here: https://github.com/breckuh/preeclampsiagwas/blob/master/snpQCreport.pdf

How to Use This Code

If you want, you can reuse this code with your own data to perform similar experiments.

You can also use it with the provided simulated data (in mockData/) which is identical to our data except simulated for privacy reasons.

If you’d like to run this code and get the exact same results as us, please contact us for our raw data files.

The data sources required are:

• data/072312_FinalReport.txt
• data/clinical.csv
• data/cardio-metabo_chip_11395247_a.csv

The format for the clinical data is contained in eopClinicalSsv.grammar.

Setup Instructions

To run the R code in this repo:

git clone https://github.com/breckuh/eopegwas
cd eopegwas
mkdir ignore
mkdir cache
mkdir output
rmarkdown::render('main.rmd')

Pvals

For some of the R notebooks, you’ll first have to run thread.r to generate the pvals for each model you want to test. thread.r will save results to the cache folder.

Phylotree

You’ll need to download and install this program: http://chibba.pgml.uga.edu/snphylo/ to run the phylotree.rmd script. Put the Phylotree scripts in the ignore folder.

Testing

Run rmarkdown::render('main.rmd') to execute the majority of the code