Genes with differential expression across ancestries are enriched in ancestry-specific disease effects likely due to gene-by-environment interactions

This repository contains raw data, preprocessing scripts, and analysis code to replicate S-LDXR analysis from Wang et al.

The project directory is organized as follows:
- `compute_de.r`: The script to compute anc-de genes
- `create_annot.100kb.sh`: code to create annotations for S-LDXR
- `create_annot.r`: R function used to create annotations for S-LDXR
- `DEstats.tgz`: Differential gene expression statistics between EAS and EUR for each 7 main cell types + PCs of each cell within each cell type
- `list_genes.txt`: Gene list as QCed as in Gazal et al. 2022 Nat Genet
- `Lupus_study_adjusted_compressed.h5ad.gz`: The single-cell dataset of Perez*, Gordon*, Subramaniam* et al. 2022 Science used in this study
- `README.sh`: This README file
- `sldxr_annotations.tgz`: Main S-LDXR annotations used in this study
- `sldxr_ref_files.tgz`: S-LDXR reference files (baseline-LD-X annotations, regression weights and EAS and EUR 1000G genotype reference files)
- `sumstats.tgz`: GWAS summary statistics of 31 traits in EAS and EUR populations
- `code_figures.tgz`: Code files for main figures