Programming Scripts for Simple and Complex Paternity Testing based on Open-Source Programming Language from the R Project

Programming scripts were written for the statistical analysis of genetic data from simple cases and complex cases of undetermined paternity. The methods presented here involve algorithms constructed with R, an open-source and increasingly popular programming language used for calculations and statistics; these methods also involve conditional probability analysis, Bayes’ Theorem, and pedigree analysis. Previous computer programs for assessing probable paternity in complex cases of undetermined paternity have been written; however, only minimal or generalized formulas are described in the papers presenting these programs. Therefore, these previously published programs are difficult to understand for most forensic researchers. Here, we present the details of the calculations used to evaluate probabilities of paternity and the details of the R scripts used execute these calculations. These scripts were constructed not only for standard trio case where DNA typing of the mother, child, and the alleged father are available, but also for more complex cases where DNA typing of the alleged father is absent. In these more complex cases, the putative genotype of the alleged father is determined from the genotypes of his parents, his siblings, his wife, children known to be his biological children, or some combination of these people. This report provides concrete and orderly descriptions of the calculations and the R scripts so that each facet of this method is easily understood. Furthermore, access to these scripts will enable individual researchers to develop calculation systems of their own.