MutationMatrix-class {Ease}

Mutation matrix

Description

A mutation matrix is used to simulate mutations that affect loci. An object of the class MutationMatrix does not only contain a (haplotypic) mutation matrix. It also contains the attributes necessary for the construction and easy-to-read display of this matrix.

Details

The mutation matrix itself is a square matrix of size equal to the number of haplotypes. It is a probability matrix in that the sum of the values in each row is equal to 1. For a given haplotype, the row associated with it describes the probabilistic proportions that lead by mutation of this haplotype to the production of the other haplotypes (and of itself if there are no mutations).

Slots

mutHapLoci

a list of haploid locus by locus allelic mulation matrices.

mutDipLoci

a list of diploid locus by locus allelic mulation matrices.

mutLoci

a list concatenating mutHapLoci and mutDipLoci

nbAlDL

a vector of the number(s) of alleles at each haploid locus

nbAlHL

a vector of the number(s) of alleles at each diploid locus

mutationMatrix

the haplotypic mutation matrix

nbHaplo

the number of haplotypes

nbDL

the number of diploid loci

nbHL

the number of haploid loci

haplotypes

the enumeration of haplotypes

IDgenome

ID of the associated genome

Author(s)

Ehouarn Le Faou