calc_LD: Calculate linkage disequilibrium between loci

In neyhartj/pbsim: Simulations of Plant Breeding Experiments

Calculate linkage disequilibrium between loci

Description

Calculates linkage disequilibrium (LD; as r^2) between loci.

Usage

calc_LD(genome, pop, loci, measure = c("r", "D"))

Arguments

genome	An object of class genome.
pop	A population.
loci	A vector of locus names for which pairwise LD should be calculated.
measure	The type of LD measurement. Can be "r2" for the squared Pearson correlation coefficient or "D" for the typical calculation using the frequency of alleles and haplotypes.

Value

A matrix of pairwise LD values.

Examples

n.mar  <- c(505, 505, 505)
len <- c(120, 130, 140)

genome <- sim_genome(len, n.mar)

# Randomly generate 15 QTL with additive allelic effects following a
# genometric series
qtl.model <- matrix(nrow = 15, ncol = 4)
genome <- sim_gen_model(genome, qtl.model, add.dist = "geometric")

# Create a random population
pop <- sim_pop(genome = genome, n.ind = 200)

# Calculate QTL allele freqencies
calc_LD(genome, pop, qtlnames(genome))

neyhartj/pbsim documentation built on Nov. 11, 2023, 4:07 p.m.