set.CADDregions {Ravages}

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)

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/

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.

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

Source

https://lysine.univ-brest.fr/RAVA-FIRST/

See Also

RAVA.FIRST, filter.adjustedCADD, burden.subscores

Examples

#Import 1000Genome data from region around LCT gene
#x <- as.bed.matrix(LCT.gen, LCT.fam, LCT.bim)

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