calculate_ld {GenomeAdmixR}

Calculate linkage disequilibrium statistics This function calculates two matrices, once containing all pairwise linkage disequilibrium (ld) values, and one matrix containing all pairwise r statistics

Description

Calculate linkage disequilibrium statistics This function calculates two matrices, once containing all pairwise linkage disequilibrium (ld) values, and one matrix containing all pairwise r statistics

Usage

calculate_ld(pop, sampled_individuals = 10, markers = NA, verbose = FALSE)

Arguments

pop

focal population

sampled_individuals

Number of individuals randomly sampled to calculate the LD matrices

markers

vector of markers. If a single number is used, that number of markers is randomly placed along the genome.

verbose

display verbose output, default is FALSE.

Value

An object containing two items:

ld_matrix

Pairwise ld statistics for all markers

rsq_matrix

Pairwise rsq statistics for all markers

Examples

wildpop =  simulate_admixture(
   module = ancestry_module(number_of_founders = 10, morgan = 1),
   pop_size = 1000,
   total_runtime = 10)

ld_results <- calculate_ld(pop = wildpop,
                           markers = 10)

plot(ld_results$ld_matrix~ld_results$dist_matrix,
     pch = 16,
     xlab="Distance between markers",
     ylab = "Linkage Disequilibrium")