ld.decay: Generate LD plot

In MoBPS: Modular Breeding Program Simulator

Description

Generate LD pot

Usage

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

Arguments

population	Population list
genotype.dataset	Genotype dataset (default: NULL - just to save computation time when get.geno was already run)
chromosomen	Only consider a specific chromosome in calculations (default: 1)
dist	Manuel input of marker distances to analyse
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

Value

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

Examples

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

Example output

#############################################################
############ Modular Breeding Program Simulator #############
#############################################################
################ Version: 1.4.87 (27-03-2020) ###############
######## To update to the most recent stable version: #######
## devtools::install_github('tpook92/MoBPS', subdir='pkg') ##
#############################################################
################ Web-interface: www.mobps.de ################
### Extended documentation: www.github.com/tpook92/MoBPS ####
#############################################################

MoBPS documentation built on Nov. 9, 2021, 5:08 p.m.