Ease (version 0.1.2)

setMutationMatrix: Setting the mutation matrix

Description

Generation of the mutation matrix associated with the genome given as input. A mutation matrix is used to simulate mutations that affect loci. An object of the class MutationMatrix does not only contain a (genotypic) mutation matrix. It also contains the attributes necessary for the construction and easy-to-read display of this matrix. The mutation matrix itself is a square matrix of size equal to the number of genotypes. It is a probability matrix in that the sum of the values in each row is equal to 1. For a given genotype, the row associated with it describes the probabilistic proportions that lead by mutation of this genotype to the production of the other genotypes (and of itself if there are no mutations).

Usage

setMutationMatrix(genomeObj, ...)

Value

a MutationMatrix object

Arguments

genomeObj

a Genome object

...

see details.

Author

Ehouarn Le Faou

Details

There are three ways to define the mutation matrix associated with a Genome class object.

1) By giving two lists of allelic mutation matrices mutHapLoci and mutDipLoci, for haploid and diploid loci respectively. Each of these lists contains as many matrices as there are loci. These matrices are transition matrices (squares, with the sum of the rows equal to 1) of size equal to the number of alleles at the locus concerned.

2) By giving a forward and a backward allelic mutation rate (forwardMut and backwardMut respectively). The generated mutation matrices will thus be defined with the same rates for all loci. A forward mutation rate means that the transition from one allele to another is done in the order in which they were defined when the Genome class object was created, and in the other direction for the backward rate.

3) By giving a list of mutations generated through the mutation function.

Examples

### Example with two loci, each with two alleles ###

# Definition of the genome
DL <- list(dl = c("A", "a"))
HL <- list(hl = c("B", "b"))
genomeObj <- setGenome(listHapLoci = HL, listDipLoci = DL)

# Three ways to define the same mutation matrix associated with the
# genome defined above:

# 1) Mutation matrix from matrices
mutHapLoci <- list(matrix(c(0.99, 0.01, 0.01, 0.99), 2))
mutDipLoci <- list(matrix(c(0.99, 0.01, 0.01, 0.99), 2))
# One can then define the MutationMatrix class object:
setMutationMatrix(genomeObj,
  mutHapLoci = mutHapLoci,
  mutDipLoci = mutDipLoci
)

# 2) Mutation matrix from mutation rates
mutMatrixObj <- setMutationMatrix(genomeObj, forwardMut = 0.1)
# or by adding a backward mutation rate:
mutMatrixObj <- setMutationMatrix(genomeObj,
  forwardMut = 1e-3,
  backwardMut = 1e-4
)

# 3) Mutation matrix from single mutation definition
mutMatrixObj <- setMutationMatrix(genomeObj,
  mutations = list(
    mutation(from = "A", to = "a", rate = 0.1),
    mutation(from = "B", to = "b", rate = 0.1)
  )
)