Rare Variant Analysis and Genetic Simulations


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Documentation for package ‘Ravages’ version 0.1.4

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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