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Wiley, Genetic Epidemiology, 6(47), p. 450-460, 2023

DOI: 10.1002/gepi.22529

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Ravages: An R package for the simulation and analysis of rare variants in multicategory phenotypes

Journal article published in 2023 by Ozvan Bocher ORCID, Gaëlle Marenne ORCID, Emmanuelle Génin ORCID, Hervé Perdry
This paper was not found in any repository, but could be made available legally by the author.
This paper was not found in any repository, but could be made available legally by the author.

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Data provided by SHERPA/RoMEO

Abstract

AbstractCurrent software packages for the analysis and the simulations of rare variants are only available for binary and continuous traits. Ravages provides solutions in a single R package to perform rare variant association tests for multicategory, binary and continuous phenotypes, to simulate datasets under different scenarios and to compute statistical power. Association tests can be run in the whole genome thanks to C++ implementation of most of the functions, using either RAVA‐FIRST, a recently developed strategy to filter and analyse genome‐wide rare variants, or user‐defined candidate regions. Ravages also includes a simulation module that generates genetic data for cases who can be stratified into several subgroups and for controls. Through comparisons with existing programmes, we show that Ravages complements existing tools and will be useful to study the genetic architecture of complex diseases. Ravages is available on the CRAN at https://cran.r-project.org/web/packages/Ravages/ and maintained on Github at https://github.com/genostats/Ravages.