R-code for calculating fluctuation assay results and 95% confidence intervals based on Ma–Sandri–Sarkar Maximum Likelihood

Abstract

The Luria–Delbrück fluctuation assay is an essential experiment in calculating mutation rates, especially in genetic and mutation research. Its reliability and accuracy have made it the go-to method for numerous researchers. In this article, we provide an R-code that statistically analyzes the assay results more easily and offers the most challenging code for calculating 95% confidence intervals based on the gold standard method “Ma–Sandri–Sarkar Maximum Likelihood.” Recently, the maximization of the likelihood function through optimization functions in R can be a challenging task. The recursive format of the likelihood function is known to cause memory stack issues. Our findings indicate that utilizing a non-recursive version of the function can increase the tractability of the maximization process. With this code, future scientists can unlock valuable statistical insights related to the biological mechanisms that drive genetic variation and can, therefore, contribute to developing novel therapeutic interventions and innovative solutions to various biological and medical challenges.