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

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

Genet Epidemiol

CESP Inserm, U1018, UFR Médecine, Univ Paris-Sud, Université Paris-Saclay, Villejuif, France.

Published: September 2023

AI Article Synopsis

  • Current software for analyzing rare variants is limited to binary and continuous traits, but Ravages provides a comprehensive R package that supports multicategory, binary, and continuous phenotypes.
  • It features functions for whole-genome association tests, leveraging C++ for efficiency, and includes both RAVA-FIRST for genome-wide variant analysis and user-defined candidate regions.
  • Ravages also has a simulation module for generating genetic data for stratified cases and controls, enhancing our ability to study the genetic basis of complex diseases, and is accessible on CRAN and GitHub.

Article Abstract

Current 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.

Download full-text PDF

Source
http://dx.doi.org/10.1002/gepi.22529DOI Listing

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