HDL

Singularity wrapper for https://github.com/zhenin/HDL

The original reference and example data are included in this repository. The referece data was extracted from .tar.gz files:

• UKB_imputed_SVD_eigen99_extraction.tar.gz - MD5 sum b1ba0081dc0f7cbf626c0e711e88a2e9
• UKB_imputed_hapmap2_SVD_eigen99_extraction.tar.gz - MD5 sum dba426aae48662ff2cb00daa246c2ade
• UKB_array_SVD_eigen90_extraction.tar.gz - MD5 sum ff3fadd7ea08bd29759b6c652618cd1f

If you use this package, please cite the original work and all reference data used in your analysis.

The history of changes is available in the CHANGELOG.md file.

Getting started

Start by following the Wiki of the original software package: https://github.com/zhenin/HDL/wiki

Here is one example and how to execute it from singularity containers:

• https://github.com/zhenin/HDL/wiki/Example-of-HDL-with-an-array-reference-panel

singularity exec --home $PWD:/home singularity/hdl.sif Rscript /tools/HDL/HDL.run.R \
gwas1.df=examples/gwas1.array.example.rds \
gwas2.df=examples/gwas2.array.example.rds \
LD.path=reference/UKB_array_SVD_eigen90_extraction \
output.file=test.Rout

which gives the following output:

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

Loading GWAS1 ...
Loading GWAS2 ...

HDL: High-definition likelihood inference of genetic correlations and heritabilities (HDL)
Version 1.4.0 (2021-04-15) 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 Wed Oct 20 10:22:51 2021
0 SNPs were removed in GWAS 1 due to missing N or missing test statistic.
0 SNPs were removed in GWAS 2 due to missing N or missing test statistic.
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.
Estimation is ongoing ... 100%

Integrating piecewise results

Point estimates:
Heritability of phenotype 1:  0.1609
Heritability of phenotype 2:  0.0131
Genetic Covariance:  -0.0101
Genetic Correlation:  -0.2206

Continuing computing standard error with jackknife
Progress... 100%

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 Wed Oct 20 10:28:16 2021 
The results were saved to test.Rout