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Ravages (version 1.2.0)

Rare Variant Analysis and Genetic Simulations

Description

Rare variant association tests: burden tests (Bocher et al. 2019 ) and the Sequence Kernel Association Test (Bocher et al. 2021 ) in the whole genome using the RAVA-FIRST approach (Bocher et al. 2022 ). Ravages also enables to perform genetic simulations (Bocher et al. 2023 ).

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Version

Install

install.packages('Ravages')

Monthly Downloads

1,196

Version

1.2.0

License

GPL-3

Maintainer

Ozvan Bocher

Last Published

February 27th, 2026

Functions in Ravages (1.2.0)

SKAT.theoretical

Multi group SKAT test using Liu et al. approximation

SKAT.continuous

Multi group SKAT test using Liu et al. approximation

Multi group SKAT test using bootstrap sampling

SKAT.permutations

Multi group SKAT test using bootstrap sampling

Linear, logistic or multinomial regression on a genetic score

bed.matrix.split.genomic.region

Bed matrix for variants associated to multiple genomic regions

adjustedCADD.annotation

SNVs and Indels annotation with adjusted CADD scores

WSS genetic score

adjustedCADD.annotation.SNVs

SNVs annotation with adjusted CADD scores

adjustedCADD.annotation.indels

Indels annotation with adjusted CADD scores

Genotypic frequencies calculation for data simulations

burden.mlogit.subscores

Logistic or multinomial regression on a multiple genetic scores within a genomic region

genes.positions

Genes positions

filter.adjustedCADD

Variant filtering based on frequency and median adjusted CADD by CADD regions

burden.continuous.subscores

Linear regression on a multiple genetic scores within a genomic region

burden.subscores

Linear, logistic or multinomial regression on a multiple genetic scores within a genomic region

filter.rare.variants

Rare variants filtering

Logistic or multinomial regression on a genetic score

burden.continuous

Linear regression on a genetic score

burden.weighted.matrix

Score matrix for burden tests

set.CADDregions

Variants annotation based on 'CADD regions' and genomic categories

set.genomic.region

Variants annotation based on gene positions

Power of RVAT based on simulations and theoretical calculations (CAST) with GRR

Exemple of functional categories

rbm.haplos.thresholds

Simulation of genetic data based on haplotypes and a libaility model

set.genomic.region.subregion

Variants annotation based on regions and subregions positions

rbm.haplos.power

Power of RVAT based on simulations with haplotypes

multinomial.asso.freq

Single variant association test with categorical phenotype

Simulation of genetic data using GRR values

rbm.haplos.freqs

Simulation of genetic data based on haplotypic frequencies

GRR matrix for genetic data simulation

LCT haplotypes data set

LCT genotypes matrix

NullObject.parameters

Null Model for SKAT and burden tests

Cohort Allelic Sum Test

GnomADgenes dataset

Kryukov data set

RAVA-FIRST: RAre Variant Association using Functionally-InfoRmed STeps