LD reference and R package repo for HDL-L

Below is a brief description of the data and code in this repository, which supports the HDL package (High-definition likelihood inference of genetic correlations and heritabilities). Here are the LD reference data for local genetic correlation analysis:

LDfile.zip: Pre-computed Linkage Disequilibrium (LD) reference data for specific genomic regions. These matrices capture the correlation structure among SNPs and are integral for local heritability and genetic correlation estimation.

bimfile.zip: Corresponding BIM files that list SNP information (e.g., chromosome, position, alleles). These files ensure proper SNP matching, QC, and alignment between the GWAS summary statistics and the LD reference panel.

Figures.zip: Codes and Data to reproduce main figures in the manuscript of HDL-L.

Simulation.zip: A collection of scripts used for simulation studies to assess the performance of HDL-L and LAVA under controlled scenarios. 

HDL.zip:  This archive provides an offline snapshot of the HDL package, mirroring the content at GitHub: https://github.com/zhenin/HDL.

compute_ld_eigen.R: An example  R script for computing and decomposing LD matrices (eigen-decomposition) from a user-provided reference panel. This script allows researchers to construct custom LD references for specialized datasets or populations.