# Rare Variant Analysis and Genetic Simulations

## Documentation for package ‘Ravages’ version 0.1.3

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

## Help Pages

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.mlogit | Logistic or multinomial regression on a genetic score
burden.weighted.matrix | Score matrix for burden tests
CAST | Cohort Allelic Sum Test
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.hap | LCT haplotypes data set
LCT.haplotypes | LCT haplotypes data set
LCT.matrix | LCT genotypes matrix
LCT.matrix.bed | LCT genotypes matrix
LCT.matrix.fam | LCT genotypes matrix
LCT.matrix.pop1000G | LCT genotypes matrix
LCT.sample | LCT haplotypes data set
LCT.snps | LCT haplotypes data set
NullObject.parameters | Null Model for SKAT and burden tests
random.bed.matrix | Simulation of genetic data using GRR values
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
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
WSS | WSS genetic score