sebrauschert / Supplement_VARPP2

Supplement: Interpretable pathogenic variant prediction for rare disease diagnostics

Authors: Sebastian Rauschert, Denise Anderson, Yiming Wang, Gareth Baynam, Timo Lassmann

Content of this repo

This repository contains the code and description to create the pathogenic and benign variant files used in the paper. Further, it contains the process as to how we get the HPO term associated genes, and how to prepare the input data for the run of VARPP2 and VARPP-RuleFit.

Sampling code

The code to sample down the number of benign variants can be found under code/sample_benign.R

Custom function from the yarn package

To take advantage of the GTExV8, we customised the downloadGTEx() function for the version 8.
The code for this can be found in code/yarn_custom.R