A user-friendly application for RAREsim, a rare-variant simulation algorithm

AUTHORS: Ryan Barnard and Nour Ibrahim
FACULTY: Megan Null
DEPARTMENT: Mathematics and Physical Sciences

ABSTRACT

Within genetics, rare variants are single nucleotide polymorphisms (SNPs) that are seen in less than 1% of the population. Identification of rare variants is important to fully understand the complexity of genetic traits and diseases. Simulation methods are crucial in the development, evaluation, and comparison of rare-variant methods. RAREsim is currently the only rare-variant simulation algorithm that simulates the expected rare-variant distribution, as seen in real data. Within RAREsim, we (1) calculate the expected distribution of rare variants, (2) simulate too many rare variants using a different simulation algorithm, and (3) probabilistically prune the number of variants to match the expected number. Through our research, we developed a Shiny application to serve as an interface for step (1), the calculation of expected rare-variant distributions (https://tinyurl.com/RAREsim). The purpose of this web app is to provide a more accessible interface for the algorithm, allowing those who are unfamiliar with the R language to use RAREsim. The app includes each function within the RAREsim R package. Additionally, users are provided with automatic graphical displays to indicate performance of the algorithm when appropriate. Within the Shiny App, individual functions are combined to provide an output table for step (1), an estimated rare-variant distribution. This table is downloaded and seamlessly integrated into the remaining 2 steps for full simulation of rare variants using RAREsim.