Example of HDL with an array reference panel

In this example, we will illustrate the use of HDL with an array reference panel. To make it convenient, the example files are already included in both the Github directory and the data folder of the R package. Therefore you do not need to download them if you have cloned HDL or installed the R package HDL. The example below uses .rds and .rda data, which have been available in the GitHub directory when you download the HDL software. If you want to test on inputting .txt files, you can download them here.

Data description

• gwas1.array.example.rds on GitHub, and gwas1.example.rda in R

  These data are based on the summary statistics from the Neale Lab round 2 GWAS of UK Biobank of birth weight. Results for 307,519 SNPs on HDL array reference panel were extracted and stored in the file.

• gwas2.array.example.rds on GitHub, and gwas2.example.rda in R

  These data are based on the summary statistics from the Neale Lab round 2 GWAS of UK Biobank of type 2 diabetes. Results for 307,519 SNPs on HDL array reference panel were extracted and stored in the file.

Estimating genetic correlation using HDL with an array reference panel

You can now follow the instruction of syntax on the wiki to get HDL results. Computation takes around 5 minutes without parallelism. With 4 cores, it takes around 1.5 minutes.

Command line user

Rscript /Path/to/HDL/HDL.run.R \
gwas1.df=/Path/to/gwas1/gwas1.array.example.rds \
gwas2.df=/Path/to/gwas2/gwas2.array.example.rds \
LD.path=/Path/to/reference/UKB_array_SVD_eigen90_extraction \
output.file=/Path/to/output/test.Rout

R user

data(gwas1.example)
data(gwas2.example)
LD.path <- "/Path/for/reference/UKB_array_SVD_eigen90_extraction"
res.HDL <- HDL.rg(gwas1.example, gwas2.example, LD.path)
res.HDL

HDL results

For how to read HDL output, please refer to the instruction on the wiki.

Function arguments:
gwas1.df=/Path/to/gwas1/gwas1.array.example.rds
gwas2.df=/Path/to/gwas2/gwas2.array.example.rds
LD.path=/Path/to/reference/UKB_array_SVD_eigen90_extraction
output.file=/Path/to/output/test.Rout

HDL: High-definition likelihood inference of genetic correlations (HDL)
Version 1.3.2 (2020-06-06) installed
Author: Zheng Ning, Xia Shen
Maintainer: Zheng Ning <zheng.ning@ki.se>
Tutorial: https://github.com/zhenin/HDL
Use citation("HDL") to know how to cite this work.

Analysis starts on Sat Jun  6 22:51:47 2020
307519 out of 307519 (100%) SNPs in reference panel are available in GWAS 1.
307519 out of 307519 (100%) SNPs in reference panel are available in GWAS 2.

Integrating piecewise results
Continuing computing standard error with jackknife


Heritability of phenotype 1:  0.1609 (0.0075) 
Heritability of phenotype 2:  0.0131 (0.0012) 
Genetic Covariance:  -0.0101 (0.0018) 
Genetic Correlation:  -0.2206 (0.0391) 
P:  1.70e-08

Analysis finished at Sat Jun  6 22:55:02 2020
The results were saved to /Path/to/output/test.Rout