gaston (version 1.2)

LD: Linkage Disequilibrium

Description

Compute Linkage Disequilibrium (LD) between given SNPs.

Usage

LD(x, lim, lim2, measure = c("r2", "r", "D"), trim = TRUE)

Value

A matrix of LD values.

Details

If lim2 is missing, the LD is computed between all SNPs with indices between lim[1] and lim[2]; else, the LD is computed between the SNPs in the range given by lim and those in the range given by lim2. Note that the LD estimates are moment estimates (which are less precise than Maximum Likelihood Estimates). If standardize(x) = "none", x will be standardized using x@mu and x@sigma. If standardize(x) = "p", the moment estimates can produce $r$ values outside of the range $[-1;1]$, hence the parameter trim. We recommend to set standardize(x) <- "mu" (trimming can still be necessary due to rounding errors).

See Also

LD.thin, LDheatmap

Examples

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

# Compute LD
ld.x <- LD(x, c(1,ncol(x)))

# Plot with LDheatmap from the package LDheatmap
LDheatmap(ld.x, genetic.distances=x@snps$pos)