WSS: WSS genetic score

In genostats/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 <- as.bed.matrix(x=LCT.matrix.bed, fam=LCT.matrix.fam, bim=LCT.snps)

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

# Filter variants with maf (computed on whole sample) < 0.025
# keeping only genomic region with at least 10 SNPs
x1 <- filter.rare.variants(x, filter = "whole", maf.threshold = 0.025, min.nb.snps = 10)

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

genostats/Ravages documentation built on Oct. 11, 2023, 11:10 p.m.