Ease (version 0.1.2)

Genome-class: Genome class

Description

The Genome class allows to define all the characteristics of the genome which will be used as a basis for the construction of transition matrices from one generation to another in simulations of the model.

Slots

listHapLoci

a list of haploid loci

listDipLoci

a list of diploid loci

recRate

a two-by-two recombination rate vector

nbHL

the number of haploid loci

nbDL

the number of diploid loci

listLoci

the list of all loci

haplotypesHL

haplotypes of haploid loci only

haplotypesDL

haplotypes of diploid loci only

haplotypes

haplotypes of all loci

alleles

the vector of all the alleles

nbAlleles

the number of alleles

nbHaplo

the number of haplotypes

IDhaplotypes

IDs of haplotypes

genotypes

the list of genotypes

nbGeno

the number of genotypes

IDgenotypes

IDs of genotypes

IDgenome

ID of the genome

Author

Ehouarn Le Faou

Details

A genome includes the list of all possible haplotypes and genotypes resulting from the combination of the alleles defined in input. As the Ease package was originally built for population genetics simulations including both diploid and haploid loci, it is necessary that both types of loci are defined. Despite this, the user can define only diploid or only haploid loci if they wish. If no diploid locus is defined, one is automatically generated with only one allele, thus not influencing the simulation. The same applies if no haploid locus is defined.

Each locus is described by a vector of factors which are the names of the possible alleles at that locus. All diploid (resp. haploid) loci thus defined are grouped in a list, called listDipLoci (resp. listHapLoci). Therefore, a Genome class object has two lists of loci defined in this way, one for diploid loci, one for haploid loci. The alleles and loci (diploid and haploid) must all have different names so that no ambiguity can persist.

If several are defined, the order of the diploid loci in the list is not trivial. The rates of two-to-one combinations between them must indeed be defined by the vector recRate. For example, if three diploid loci are defined, recRate must be of length 2, the first of its values defining the recombination rate between the first and second loci, the second of its values the recombination rate between the second and third loci. For example, if we want to define two groups of two loci that are linked to each other but are on two different chromosomes, we can define a recRate = c(0.1, 0.5, 0.1). The first two loci are thus relatively linked (recombination rate of 0.1), as are the last two loci. On the other hand, the recombination rate of 0.5 between the second and third loci ensures that the two groups are independent.