Ravages (version 1.2.0)

set.CADDregions: Variants annotation based on 'CADD regions' and genomic categories

Description

Attributes CADD regions and genomic categories to variants based on their positions

Usage

set.CADDregions(x, verbose = T, path.data, build = c("b37", "b38"))

Value

The same bed matrix as x with three additional columns :

genomic.region

The CADD region of each variant

SubRegion

The genomic category of each variant among 'Coding', 'Regulatory' or 'Intergenic'

adjCADD.Median

The median of adjusted CADD of variants observed at least to times in GnomAD genomes r2.0.1

Arguments

x

A bed.matrix

verbose

Whether to display information about the function actions

path.data

The repository where data for RAVA-FIRST are or will be downloaded from https://lysine.univ-brest.fr/RAVA-FIRST/

build

The build of the data, either "b37" or "b38". The CADD Regions in the corresponding build will be considered

Details

To attribute variants to CADD regions and genomic categories, the files "CADDRegions.2021.hg19.bed.gz" and "FunctionalAreas.hg19.bed.gz" will be downloaded from https://lysine.univ-brest.fr/RAVA-FIRST/ in the repository of the package Ravages. CADD regions are non-overlapping regions that have been defined in the whole genome to perform rare variant association tests in the RAVA.FIRST() pipeline. It is recommended to use this function chromosome by chromosome for large datasets for time and memory managment.

See Also

RAVA.FIRST, filter.adjustedCADD, burden.subscores

Examples

#Import data in a bed matrix (example in build 37)
#x <- read.bed.matrix( system.file("extdata", "LCT.EUR.b37.bed", package="Ravages") )

#Group variants within CADD regions and genomic categories
#x <- set.CADDregions(x, build = "b37")
#table(x@snps$genomic.region) #CADD regions
#table(x@snps$SubRegion) #Genomic categories