setMutationModel: Set a mutation model
In pedprobr: Probability Computations on Pedigrees

Description Usage Arguments Details Value Examples

View source: R/setMutationModel.R

This function offers a convenient way to attach mutation models to a pedigree with marker data. It wraps pedmut::mutationModel(), which does the main work of creating the models, but relieves the user from having to loop through the markers in order to supply the correct alleles and frequencies for each marker.

1	setMutationModel(x, markers = NULL, model, ...)

`x`	A `ped` object or a list of such.
`markers`	A vector of names or indices referring to markers attached to `x`. (Default: All markers.)
`model`	A model name implemented by `pedmut::mutationModel()`. See Details.
`...`	Arguments forwarded to `pedmut::mutationModel()`, e.g., `rate`.

Currently, the following models are implemented in the pedmut package:

equal : All mutations equally likely; probability 1-rate of no mutation
proportional : Mutation probabilities are proportional to the target allele frequencies
onestep: A mutation model for microsatellite markers, allowing mutations only to the nearest neighbours in the allelic ladder. For example, '10' may mutate to either '9' or '11', unless '10' is the lowest allele, in which case '11' is the only option. This model is not applicable to loci with non-integral microvariants.
stepwise: A common model in forensic genetics, allowing different mutation rates between integer alleles (like '16') and non-integer "microvariants" like '9.3'). Mutations also depend on the size of the mutation if the parameter 'range' differs from 1.
custom : Allows any mutation matrix to be provided by the user, in the matrix parameter
random : This produces a matrix of random numbers, where each row is normalised so that it sums to 1
trivial : The identity matrix; i.e. no mutations are possible.

An object similar to x.

### Example requires the pedmut package ###
if (requireNamespace("pedmut", quietly = TRUE)){

# A pedigree with data from a single marker
x = nuclearPed(1)
x = setMarkers(x, marker(x, geno = c("a/a", NA, "b/b"))) # mutation!

# Set `equal` model
x = setMutationModel(x, marker = 1, model = "equal", rate = 0.01)

# Inspect model
mutmod(x, 1)

# Likelihood
likelihood(x, 1)

}