Ravages (version 1.2.0)

CAST: Cohort Allelic Sum Test

Description

Calculates the CAST genetic score

Usage

CAST(x, genomic.region = x@snps$genomic.region, maf.threshold = 0.5, 
     flip.rare.alleles = T)

Value

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

Arguments

x

A bed.matrix

genomic.region

A factor defining the genomic region of each variant

maf.threshold

The MAF used for the definition of a rare variant, set at 0.5 by default, i.e. all variants are kept

flip.rare.alleles

Whether to flip the A1/A2 alleles if the A1 allele is rare, set at T by default

Details

By default, CAST counts if an individual carries at least one rare allele in the genomic region. If flip.rare.alleles = F and the reference allele A1 is rare, the alles A1 and A2 won't be flipped and CAST will count the number of alternative alleles A2.

References

Morgenthaler S and Thilly WG. A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: a cohort allelic sums test (CAST). Mutat Res. 2007

See Also

WSS, 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 CAST
score.CAST <- CAST(x1, maf.threshold=0.025)