filter.rare.variants {Ravages}

Rare variants filtering

Description

Filter rare variants based on a MAF threshold and a given number of SNP or a given cumulative MAF per genomic region

Usage

filter.rare.variants(x, ref.level = NULL, filter=c("whole", "controls", "any"), 
                     maf.threshold=0.01, min.nb.snps = 2, min.cumulative.maf = NULL, 
                     group = NULL, genomic.region = NULL)

Arguments

x

A bed.matrix

ref.level

The level corresponding to the controls group, only needed if filter=="controls"

filter

On which group the filter will be applied

maf.threshold

The MAF threshold used to define a rare variant, set at 0.01 by default

min.nb.snps

The minimum number of variants needed to keep a genomic region, set at 2 by default

min.cumulative.maf

The minimum cumulative maf of variants needed to keep a genomic region

group

A factor indicating the group of each individual, only needed if filter = "controls" or filter = "any". If missing, x@ped$pheno is taken

genomic.region

An optional factor containing the genomic region of each variant, only needed if min.nb.snps or min.cumulative.maf is specified and if x@snps$genomic.region doesn't exist

Details

To use this function, a factor 'genomic.region' should be present in the slot x@snps.

If filter="whole", only the variants having a MAF lower than the threshold in the entire sample are kept.

If filter="controls", only the variants having a MAF lower than the threshold in the controls group are kept.

If filter="any", only the variants having a MAF lower than the threshold in any of the groups are kept.

Value

A bed.matrix with filtered variants

Examples

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

#Group variants within known genes
x <- set.genomic.region(x)
table(x@snps$genomic.region, useNA="ifany")
                             
#Filter of rare variants: only non-monomorphic variants with 
#a MAF lower than 2.5%
#keeping only genomic regions with at least 10 SNPs
x1 <- filter.rare.variants(x, filter = "whole", maf.threshold = 0.025, min.nb.snps = 10)
table(x1@snps$genomic.region, useNA="ifany")

#Keep only variants with a MAF<2%
#and regions with a cumulative MAF>10%
filter.rare.variants(x, filter = "whole", maf.threshold = 0.02, min.nb.snps = 1, 
                     min.cumulative.maf=0.2)