R code for the GTEx analysis for the article "Enhancer Release and Retargeting activates disease genes", Nature, 2021 , https://doi.org/10.1038/s41586-021-03577-1
ERR_finder.R is the script that searches for enhancer-promoter connections using GTEx v7 eQTL data.
The script requires R packages 'tidyverse' and bioconductor package 'GenomicRanges' for running.
Annotation files required for running the script are included in the folder 'ERR-datafiles' can be found at https://www.dropbox.com/sh/5t80oqgu0sbtgx3/AAAwY2EIqhIhRzX7exMn2Ta6a?dl=0
Mandatory input files:
gencode_info.txt: File containing GENCODE gene annotations
combinedEnhancerAnnotations.txt: Enhancer annotations from HEDD database (http://zdzlab.einsteinmed.org/1/hedd.php)
v7_eqtl_data: Tissue specific eQTL data from GTEx v7 release