setSelectNeutral: Setting the selection

In Ease: Simulating Explicit Population Genetics Models

Setting the selection

Description

Generation of a neutral class Selection object. It can be used as a basis for adding selection layers with the setSelectOnInds, setSelectOnGametes or setSelectOnGametesProd functions, or if the model is neutral.

Usage

setSelectNeutral(genomeObj)

Arguments

genomeObj

a Genome object

Details

An object of type Selection is an object which describes the set of fitnesses which will be taken into account in the simulations. The selection according to these fitnesses can be applied at three levels: at the level of the individual, at the level of the production of gametes and at the level of the gametes themselves. Selection is therefore genotypic in the first two cases (each genotype is associated with a fitness value) and haplotypic in the third (each haplotype is associated with a fitness value).

Value

a Selection object

Author(s)

Ehouarn Le Faou

Examples

### Example with two loci, each with two alleles ###
# Definition of the diploid locus
DL <- list(dl = c("A", "a"))
# Definition of the haploid locus
HL <- list(hl = c("B", "b"))
# Definition of the object of Genome class
genomeObj <- setGenome(listHapLoci = HL, listDipLoci = DL)
genomeObj

### Exemple with more diploid loci ###
# Definition of the diploid loci
DL <- list(
  dl1 = c("A", "a"),
  dl2 = c("B", "b"),
  dl3 = c("C", "c")
)
# Definition of the haploid locus
HL <- list(hl = c("D", "d"))
# Definition of the object of Genome class, with in addition the necessary
# definition of recombination rates between loci:
genomeObj <- setGenome(
  listHapLoci = HL, listDipLoci = DL,
  recRate = c(0.1, 0.5)
)
# Here we have a 0.1 recombination rate between dl1 and dl2 and a 0.5
# recombination rate between dl2 and dl3. It is as if dl1 and dl2 were linked,
# for example on the same chromosome, and that dl2 (and dl1 by consequence)
# and dl3 were independent, for example on different chromosomes.

genomeObj

Ease documentation built on Nov. 10, 2022, 5:54 p.m.