For the LD, HWE, CATT and FET GWAS, the project will require a database (i.e., MySql) where we will be keeping the genomics data. We generate random synthetic data from the SNP frequency file (freq_refined.txt). The sql file for the current results can be found in 'genomic_data.sql' file.
The code will need a persistence.xml file (as it uses Eclipse Persistence) that should contain the database connection parameters: hostname, username and password to the database.
To generate new data, use the main java files in insertion package.
The global and local model both will get their data from a table named gwas_original_local (rename it if needed in DB.GwasPlaintext.java). The global model is available in cs.umanitoba.ca.dpbinpacking.GWASDP as there are four functions that will give the accuracy results:
- calculateLD (TargetSNP)
- calculateHWE (TargetSNP)
- calculateCATT (TargetSNPCase, TargetSNPControl)
- calculateFET (TargetSNPCase, TargetSNPControl)
The epsilon values can be changed in the java file as well. The noise values are added to the statistics all handled from GWASDP.java.
The local model can be executed from GWASLocalLapDP.java and GWASLocalRRDP.java for the Laplace and Randomized Response method in cs.umanitoba.ca.dpbinpacking package. These operate on differet tables in the database which are also included on the genomic_db.sql file.
For any queries please email azizmma at cs.umanitoba.ca