Pgainsim: an R-package to assess the mode of inheritance for quantitative trait loci in GWAS.

Abstract

MotivationWhen performing genome-wide association studies conventionally the additive genetic model is used to explore whether a single nucleotide polymorphism (SNP) is associated with a quantitative trait. But for variants, which do not follow an intermediate mode of inheritance (MOI), the recessive or the dominant genetic model can have more power to detect associations and furthermore the MOI is important for downstream analyses and clinical interpretation. When multiple MOIs are modelled the question arises, which describes the true underlying MOI best.ResultsWe developed an R-package allowing for the first time to determine study specific critical values when one of the three models is more informative than the other ones for a quantitative trait locus. The package allows for user-friendly simulations to determine these critical values with predefined minor allele frequencies and study sizes. For application scenarios with extensive multiple testing we integrated an interpolation functionality to determine critical values already based on a moderate number of random draws.Availability and implementationThe R-package pgainsim is freely available for download on Github at https://github.com/genepi-freiburg/pgainsim.Supplementary informationSupplementary data are available at Bioinformatics online.