WSS: WSS genetic score

In Ravages: Rare Variant Analysis and Genetic Simulations

WSS genetic score

Description

Caluclates the WSS genetic score

Usage

WSS(x, genomic.region = x@snps$genomic.region)

Arguments

x	A bed.matrix
genomic.region	A factor containing the genomic region of each variant

Value

A matrix containing the WSS genetic score with one row per individual and one column per genomic.region

References

Madsen E and Browning S. A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic. PLoS Genet. 2009

See Also

CAST, burden.weighted.matrix, burden.mlogit

Examples

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

#Group variants within known genes
x <- set.genomic.region(x)

#Filter of rare variants: only non-monomorphic variants with
#a MAF lower than 2.5%
#keeping only genomic regions with at least 10 SNP
x1 <- filter.rare.variants(x, filter = "whole", maf.threshold = 0.025, min.nb.snps = 10)

# Compute burden score WSS
score.WSS <- WSS(x1)

Ravages documentation built on Feb. 27, 2026, 5:08 p.m.