# Rare Variant Analysis and Genetic Simulations

## Documentation for package ‘Ravages’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

adjustedCADD.annotation | SNVs and Indels annotation with adjusted CADD scores
adjustedCADD.annotation.indels | Indels annotation with adjusted CADD scores
adjustedCADD.annotation.SNVs | SNVs annotation with adjusted CADD scores
bed.matrix.split.genomic.region | Bed matrix for variants associated to multiple genomic regions
burden | Linear, logistic or multinomial regression on a genetic score
burden.continuous | Linear regression on a genetic score
burden.continuous.subscores | Linear regression on a multiple genetic scores within a genomic region
burden.mlogit | Logistic or multinomial regression on a genetic score
burden.mlogit.subscores | Logistic or multinomial 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
burden.weighted.matrix | Score matrix for burden tests
CAST | Cohort Allelic Sum Test
filter.adjustedCADD | Variant filtering based on frequency and median adjusted CADD by CADD regions
filter.rare.variants | Rare variants filtering
genes.b37 | Genes positions
genes.b38 | Genes positions
genes.positions | Genes positions
genotypic.freq | Genotypic frequencies calculation for data simulations
GnomADgenes | GnomADgenes dataset
GRR.matrix | GRR matrix for genetic data simulation
Jaccard | Jaccard index
Kryukov | Kryukov data set
LCT.EUR.b37 | LCT genotypes matrix
LCT.EUR.b37.bed | LCT genotypes matrix
LCT.EUR.b37.fam | LCT genotypes matrix
LCT.EUR.b38 | LCT genotypes matrix
LCT.EUR.b38.bed | LCT genotypes matrix
LCT.EUR.b38.fam | LCT genotypes matrix
LCT.hap | LCT haplotypes data set
LCT.haplotypes | LCT haplotypes data set
LCT.sample | LCT haplotypes data set
LCT.snps | LCT haplotypes data set
multinomial.asso.freq | Single variant association test with categorical phenotype
NullObject.parameters | Null Model for SKAT and burden tests
RAVA.FIRST | RAVA-FIRST: RAre Variant Association using Functionally-InfoRmed STeps
rbm.GRR | Simulation of genetic data using GRR values
rbm.GRR.power | Power of RVAT based on simulations and theoretical calculations (CAST) with GRR
rbm.haplos.freqs | Simulation of genetic data based on haplotypic frequencies
rbm.haplos.power | Power of RVAT based on simulations with haplotypes
rbm.haplos.thresholds | Simulation of genetic data based on haplotypes and a libaility model
set.CADDregions | Variants annotation based on 'CADD regions' and genomic categories
set.genomic.region | Variants annotation based on gene positions
set.genomic.region.subregion | Variants annotation based on regions and subregions positions
SKAT | SKAT test
SKAT.bootstrap | Multi group SKAT test using bootstrap sampling
SKAT.continuous | Multi group SKAT test using Liu et al. approximation
SKAT.permutations | Multi group SKAT test using bootstrap sampling
SKAT.theoretical | Multi group SKAT test using Liu et al. approximation
subregions.LCT | Exemple of functional categories
WSS | WSS genetic score