Randomized HE regression estimator

We propose a scalable randomized Method-of-Moments (MoM) estimator of SNP heritability and genetic correlations in LMMs. Our method, RHE-reg, leverages the structure of genotype data to obtain runtimes that are sub-linear in the number of individuals (assuming the number of SNPs is held constant).

If you find that this software is useful for your research project, please cite our paper:

Wu Y.,Sankararaman S. (2018) A scalable estimator of SNP heritability for Biobank-scale Data

Randomized genetic correlation estimator

We propose a scalable randomized Method-of-Moments (MoM) estimator of genetic correlations in bi-variate LMMs. The method compute genetic correlation in two senerios: the samples of phenotypes are shared and partially shared.

If you find that this software is useful for your research project, please cite our paper:

Wu, Y., Yaschenko, A., Heydary, M. H., & Sankararaman, S. (2019). Fast estimation of genetic correlation for Biobank-scale data. bioRxiv, 525055.

The following packages are required on a linux machine to compile and use the software package.

g++
cmake
make

Installing RHE_reg is fairly simple. Follow the following steps:

git clone https://github.com/ariel-wu/RHE_reg.git
cd RHE_reg
mkdir build 
cd build
cmake .. 
make

After compiling the executble fastppca is present in the build directory. To run RHE_reg, use

*./RHE_reg <command_line arguments>

The values in the brackets are the command line flags for running the code without parameter file.

* genotype (-g) : The path of the genotype file or plink binary file prefix.
* phenotype (-p) : The path of the phenotype file. 
* covariate (-c) : The path of the covariate file.
* covariate name (-cn) : The name of the covariate to use in the covariate file. 
  If not specified, RHE_reg will use all the covarites in the covariate file. 
* batch number (-b) : Number of random vectors used in the estimator % 10. 
* phenotype number (-mpheno) : The number of phenotype to use in the phenotype file. 
  If not specified, RHE_reg will compute heritability estimates on all the phenotypes. 
* fill in missing phenotype with mean (-fill) : Fill in missing phenotypes with mean. 
* Computing genetic correlation only (noh2g): If pass in multiple phenotypes, the program will compute genetic correlation factors (rg). If the phenotypes share samples, one may compute genetic correlation without computing heritabitliy. This option must be combined with (-fill) if there is missingess in phenotypes.  
  Otherwise will be ignored. 

An example parameter file is provided in the example directory. You can run the code using the command: To compute heritability and genetic correlation:

../build/RHE_reg -g 200_100 -p 200_100.pheno.plink -c 200_100.cov -b 10 

To compute heritability and genetic correlation for shared-sample phenotypes:

../build/RHE_reg -g 200_100 -p 200_100.pheno.pheno2 -fill -b 10

To compute genetics correlation only for shared-sample phenotypes:

../build/RHE_reg -g 200_100 -p 200_100.pheno_pheno2 -fill -noh2g -b 10