locus-class: Create a locus

In frederic-michaud/hapex: FRequency Evolution Simulator of Sex-linked Alleles

Description

A locus is a S4 class which define all the properties of a locus, like the various possible allele and genotype, related fitness and sex-determination system.

Arguments

allele1	The allele on the first chromosome
allele2	The allele on the second chromosome
fitness.male	Optional: The fitness of the males carrying this genotype
fitness.female	Optional: The fitness of the female carrying this genotype
sd	Optional: The proportion of individual with this genotype which are male (0 mean that it's always a female and 1 it's always a male)
recombination.modifier	Optional: indicate how this genotype modify the overall recombination rate of the chromosome
name	The name of the allele. Notice that this vector is of different size as the ones before.

Details

Notice that to create a locus, all possible genotype should be included. Expect for the parameter 'allele.name', all vector should have the same length, and more specifically, the length of the number of possible genotype at this locus. The reason it is like this, is that it allows to skip some genotypes (like yy) and specify easly the fitness of all genotype without using dominance factor.

Examples

locus1 = create.locus(allele1 = c(1,1),
                                allele2 = c(1,2),
                                    sd = c(0,1),
                          fitness.male = c(1,1),
                        fitness.female = c(1,1),
                           allele.name = c("x","y"))

frederic-michaud/hapex documentation built on May 15, 2019, 3:29 p.m.