gaston (version 1.2)

LD.thin: LD thinning

Description

Select SNPs in LD below a given threshold.

Usage

LD.thin(x, threshold, max.dist = 100e3, beg = 1, end = ncol(x),
        dist.unit = c("bases", "indices"), extract = TRUE,
        keep = c("left", "right", "random"))

Value

If extract = TRUE, a bed.matrix extracted from x with SNPs in pairwise LD below the given threshold. If extract = FALSE, a logical vector of length end - beg + 1, where TRUE indicates that the corresponding SNPs is selected.

Details

The SNPs to keep are selected by a greedy algorithm. The LD is computed only for SNP pairs for which distance is inferior to max.dist, expressed in number of bases if dist.unit = "bases", or in number of SNPs if dist.unit = "indices". The algorithm tries to keep a maximum number of SNPs: it is not appropriate to select tag-SNPs.

See Also

LD

Examples

# Load data
data(TTN)
x <- as.bed.matrix(TTN.gen, TTN.fam, TTN.bim)

# Select SNPs in LD r^2 < 0.4, max.dist = 500 kb
x <- set.stats(x)
y <- LD.thin(x, threshold = 0.4, max.dist = 500e3)
y

# Verifies that there is no SNP pair with LD r^2 > 0.4
# (note that the matrix ld.y has ones on the diagonal)
ld.y <- LD( y, lim = c(1, ncol(y)) )
sum( ld.y > 0.4 )