This contains Python codes used in our experiments on methods for privately releasing the top K significant marker loci based on linkage analysis using a transmission disequilibrium test (TDT). We applied the Laplace mechanism and the exponential mechanism, which is based on the concept of differential privacy (DP).
We conducted experiments based on simulation data to evaluate the runtime of our algorithms and the accuracy of outputs. The distribution of the statistics on our datasets can be found in the datasets file.
Supplements.pdf contains detailed proofs and detailed description of our datasets.
For details of our releasing methods and experimental results, please see our paper entitled "Differentially Private Linkage Analysis with TDT --- the case of two affected children per family" (https://doi.org/10.1109/bibm52615.2021.9669365) presented at IEEE BIBM 2021.
Errata:
・p.766. Definition 4. "
Akito Yamamoto
Division of Medical Data Informatics, Human Genome Center,
the Institute of Medical Science, the University of Tokyo