Rare Variant Analysis and Genetic Simulations

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Documentation for package ‘Ravages’ version 1.1.3

• 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.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
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