BridgePRS download comes with example toy data in the folders data/pop_AFR, data/pop_EUR and data/pop_EAS. Each directory contains (1) GWAS summary statistic files, (2) genotype files (plink binary format), and (3) phenotype files (txt format). A continuous and binary phenotype are given in the phenotype files, both phenotypes use the same summary statistics, For more information on file type requirements or how to create population configuration files for your own data, see Guide: Input Data.

BridgePRS uses configuation files which contain the information of the populations being analysed: the population name, paths for the input data and the column headers of the summary statistics files. Three example configuations files are provided, one for each population: data/eur.config, data/afr.config, data/eas.config. These files

Run the demo:

To analyses the continuous trait (y)

./bridgePRS pipeline go -o out1 --config_files data/afr.config data/eur.config --phenotype y 

After this runs successfully, you can analyze the binary phenotype "y.binary" with the following command:

./bridgePRS pipeline go -o out2 --config_files data/afr.config data/eur.config --phenotype y.binary

Results:

Please see the next page for interpretation of the result on the toy data.