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Ravages (version 1.1.3)

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; and genetic simulations.

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Version

Install

install.packages('Ravages')

Monthly Downloads

260

Version

1.1.3

License

GPL-3

Maintainer

Ozvan Bocher

Last Published

March 28th, 2023

Functions in Ravages (1.1.3)

Kryukov

Kryukov data set
NullObject.parameters

Null Model for SKAT and burden tests
SKAT

SKAT test
LCT.matrix

LCT genotypes matrix
LCT.haplotypes

LCT haplotypes data set
RAVA.FIRST

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

GnomADgenes dataset
Jaccard

Jaccard index
WSS

WSS genetic score
SKAT.theoretical

Multi group SKAT test using Liu et al. approximation
SKAT.permutations

Multi group SKAT test using bootstrap sampling
adjustedCADD.annotation

SNVs and Indels annotation with adjusted CADD scores
adjustedCADD.annotation.SNVs

SNVs annotation with adjusted CADD scores
burden

Linear, logistic or multinomial regression on a genetic score
adjustedCADD.annotation.indels

Indels annotation with adjusted CADD scores
bed.matrix.split.genomic.region

Bed matrix for variants associated to multiple genomic regions
SKAT.bootstrap

Multi group SKAT test using bootstrap sampling
SKAT.continuous

Multi group SKAT test using Liu et al. approximation
burden.weighted.matrix

Score matrix for burden tests
burden.mlogit

Logistic or multinomial regression on a genetic score
filter.adjustedCADD

Variant filtering based on frequency and median adjusted CADD by CADD regions
burden.subscores

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

Linear regression on a genetic score
genes.positions

Genes positions
genotypic.freq

Genotypic frequencies calculation for data simulations
filter.rare.variants

Rare variants filtering
burden.mlogit.subscores

Logistic or multinomial regression on a multiple genetic scores within a genomic region
burden.continuous.subscores

Linear regression on a multiple genetic scores within a genomic region
subregions.LCT

Exemple of functional categories
set.CADDregions

Variants annotation based on 'CADD regions' and genomic categories
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
rbm.haplos.freqs

Simulation of genetic data based on haplotypic frequencies
rbm.haplos.thresholds

Simulation of genetic data based on haplotypes and a libaility model
set.genomic.region

Variants annotation based on gene positions
rbm.GRR.power

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

Simulation of genetic data using GRR values
GRR.matrix

GRR matrix for genetic data simulation
CAST

Cohort Allelic Sum Test