README.md

• 1-reformat-data.R is the R script that preps datasets in simulated-data for MB-MDR runs. It writes the reformated train/test datasets in reformatted-data/.

• 2-run-mb-mdr.sh executes mbmdr-4.4.1-mac-64bits.out --- the MBMDR-4.4.1 software that can be downloaded here --- and writes results to mb-mdr/results/. Note that one of the important options that affect computation time is -n of which default is 1000.

Run this code with ./2-run-mb-mdr.sh. There are two result files per dataset: output that contains the SNP combinations and their corresponding statistics and model that contains the HLO matrices of all SNP combinations.

• The 3*.Rmd files parse the MB-MDR results in mb-mdr/results/, compute the multilocus risk scores (MRS) and write them to mb-mdr/risks/. kd indicates k-way interactions within the SNP combinations.

• mb-mdr/documentation/ contains documentation and papers related to the MB-MDR software.