MoBPS (version 1.13.1)

ld.decay: 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
)

Value

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

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

Examples

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