This is a command line tool based on R programming language for lassosum2. This is a simplified version of lassosum2 implemented in PROSPER. Please be careful if using it separately. Please contact Jingning Zhang ([email protected]) if you have any questions.
The required scripts, LD reference panels, R packages, and inputs are same as PROSPER.
A toy example is provided also in the last section of README.md on the website of PROSPER.
Example codes for running lassosum2 in both EUR and AFR populations:
package='/dcs04/nilanjan/data/jzhang2/MEPRS/pacakge/try_from_github/PROSPER'
path_example='/dcs04/nilanjan/data/jzhang2/MEPRS/pacakge/try_from_github/PROSPER/example/'
path_result='/dcs04/nilanjan/data/jzhang2/MEPRS/pacakge/try_from_github/PROSPER/PROSPER_example_results/'
path_plink='/dcs04/nilanjan/data/jzhang2/TOOLS/plink/plink2'
mkdir ${path_result}
Rscript ${package}/scripts/lassosum2.R \
--PATH_package ${package} \
--PATH_out ${path_result}/lassosum2 \
--PATH_plink ${path_plink} \
--FILE_sst ${path_example}/summdata/EUR.txt,${path_example}/summdata/AFR.txt \
--pop EUR,AFR \
--chrom 1-22 \
--bfile_tuning ${path_example}/sample_data/EUR/tuning_geno,${path_example}/sample_data/AFR/tuning_geno \
--pheno_tuning ${path_example}/sample_data/EUR/pheno.fam,${path_example}/sample_data/AFR/pheno.fam \
--bfile_testing ${path_example}/sample_data/EUR/testing_geno,${path_example}/sample_data/AFR/testing_geno \
--pheno_testing ${path_example}/sample_data/EUR/pheno.fam,${path_example}/sample_data/AFR/pheno.fam \
--testing TRUE \
--NCORES 5
Please direct any problems or questions to Jingning Zhang ([email protected]).