calculate_LD: Calculate LD statistics

In thijsjanzen/isoSIM: Simulate Linkage Disequilibrium Along Chromosomes in Isofemale Lines

Description

This function calculates two matrices, once containing all pairwise LD values, one containing all pairwise r statistics

Usage

calculate_LD(pop, sampled_individuals,
                    number_of_markers, random_markers)

Arguments

pop	Focal population
sampled_individuals	Number of individuals randomly sampled to calculate the LD matrices
number_of_markers	Number of markers used to calculate the LD matrices
random_markers	If TRUE, markers are randomly spaced along the chromosome, if FALSE, markers are equidistantly spaced along the chromosome.

Value

An object containing two items:

LD_matrix	Pairwise LD statistics for all markers
rsq_matrix	Pairwise rsq statistics for all markers

Author(s)

Thijs Janzen

Examples

## Not run: 
  wildpop =  create_population(pop_size = 100,
                             number_of_founders = 10,
                             total_runtime = 1000,
                             morgan = 1,
                             seed = 42,
                             write_to_file = FALSE)

  LD_results <- calculate_LD(wildpop,
                                    number_of_markers = 10,
                                    random_markers = TRUE)
  
## End(Not run)

thijsjanzen/isoSIM documentation built on May 29, 2019, 10:39 a.m.