breeding.intern7: Internal function to simulate one meiosis

In MoBPS: Modular Breeding Program Simulator

Internal function to simulate one meiosis

Description

Internal function to simulate one meiosis

Usage

breeding.intern7(
  info.parent,
  parent,
  population,
  mutation.rate = 10^-5,
  remutation.rate = 10^-5,
  recombination.rate = 1,
  recom.f.indicator = NULL,
  duplication.rate = 0,
  duplication.length = 0.01,
  duplication.recombination = 1,
  delete.same.origin = FALSE,
  gene.editing = FALSE,
  nr.edits = 0,
  gen.architecture = 0,
  decodeOriginsU = MoBPS::decodeOriginsR,
  recombination.function = MoBPS::recombination.function.haldane,
  dup_activ = TRUE,
  rt_activ = TRUE,
  grandsib_activ = TRUE
)

Arguments

info.parent	position of the parent in the dataset
parent	list of information regarding the parent
population	Population list
mutation.rate	Mutation rate in each marker (default: 10^-5)
remutation.rate	Remutation rate in each marker (default: 10^-5)
recombination.rate	Average number of recombination per 1 length unit (default: 1M)
recom.f.indicator	Use step function for recombination map (transform snp.positions if possible instead)
duplication.rate	Share of recombination points with a duplication (default: 0 - DEACTIVATED)
duplication.length	Average length of a duplication (Exponentially distributed)
duplication.recombination	Average number of recombinations per 1 length uit of duplication (default: 1)
delete.same.origin	If TRUE delete recombination points when genetic origin of adjacent segments is the same
gene.editing	If TRUE perform gene editing on newly generated individual
nr.edits	Number of edits to perform per individual
gen.architecture	Used underlying genetic architecture (genome length in M)
decodeOriginsU	Used function for the decoding of genetic origins [[5]]/[[6]]
recombination.function	Function used to calculate position of recombination events (default: MoBPS::recombination.function.haldane())
dup_activ	Internal parameter to check if duplications have to be simulated
rt_activ	Internal parameter to check if RTs have to be simulated
grandsib_activ	Internal parameter to check if grandsibling contributions have to be calculated

Value

Inherited parent gamete

Examples

data(ex_pop)
child_gamete <- breeding.intern7(info.parent = c(1,1,1), parent = ex_pop$breeding[[1]][[1]][[1]],
                                population = ex_pop)

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