ld.decay: Generate LD plot

In MoBPS: Modular Breeding Program Simulator

Generate LD plot

Description

Generate LD pot

Usage

ld.decay(
  population,
  genotype.dataset = NULL,
  chromosome = 1,
  dist = NULL,
  step = 5,
  max = 500,
  max.cases = 100,
  database = NULL,
  gen = NULL,
  cohorts = NULL,
  type = "snp",
  plot = FALSE,
  xlim = NULL,
  ylim = NULL
)

Arguments

population	Population list
genotype.dataset	Genotype dataset (default: NULL - just to save computation time when get.geno was already run)
chromosome	Only consider a specific chromosome in calculations (default: 1)
dist	Manuel input of marker distances to analyze
step	Stepsize to calculate LD
max	Maximum distance between markers to consider for LD-plot
max.cases	Maximum number of marker pairs to consider of each distance (default: 100; randomly sampled!)
database	Groups of individuals to consider for the export
gen	Quick-insert for database (vector of all generations to export)
cohorts	Quick-insert for database (vector of names of cohorts to export)
type	Compute LD decay according to following distance measure between markers (default: "snp", alt: "bp", "cM")
plot	Set to FALSE to not generate an LD plot
xlim	Axis limits for the x-axis in the LD plot
ylim	Axis limits for the y-axis in the LD plot

Value

LD-decay plot for in gen/database/cohorts selected individuals

Examples

data(ex_pop)
ld.decay(population=ex_pop, gen=5)

MoBPS documentation built on Nov. 5, 2025, 6:26 p.m.