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Ravages: An R package for the simulation and analysis of rare variants in multicategory phenotypes.
Genet. Epidemiol. 47, 450-460 (2023)
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.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
R Package ; Multicategory Phenotypes ; Rare Variants ; Simulations ; Whole-genome; Power Analysis; Association
ISSN (print) / ISBN
0741-0395
e-ISSN
1098-2272
Journal
Genetic Epidemiology
Quellenangaben
Volume: 47,
Issue: 6,
Pages: 450-460
Publisher
Wiley
Publishing Place
111 River St, Hoboken 07030-5774, Nj Usa
Non-patent literature
Publications
Reviewing status
Peer reviewed
Institute(s)
Institute of Translational Genomics (ITG)