MoBPS (version 1.13.1)

breeding.intern7: 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
)

Value

Inherited parent gamete

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

Examples

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