setMutmod: Set a mutation model

In pedtools: Creating and Working with Pedigrees and Marker Data

Set a mutation model

Description

This function offers a convenient way to set or modify mutation models to markers attached to a pedigree. 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.

Usage

setMutmod(x, markers = NULL, ..., update = FALSE)

Arguments

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.)
...	Arguments forwarded to pedmut::mutationModel(), e.g., model, rate, etc.
update	A logical. If TRUE, existing mutation models (if present) are updated with the parameters specified in .... If FALSE (default), any previous models are ignored, and new mutation models are created from the parameters in ....

Details

Currently, the following models are supported:

• equal: All mutations equally likely; probability 1 - rate of no mutation

• proportional: Mutation probabilities are proportional to the target allele frequencies

• onestep: A simple model for microsatellite markers, in which mutations are only allowed 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). Not applicable to loci with non-integral microvariants.

• stepwise: A common model for microsatellite markers. Mutation rates depend on the step size in the allelic ladder, and also the allelic classes: integral repeats like '16', versus non-integer microvariants like '16.3'.

• 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; no mutations are possible

Value

An object similar to x.

Examples

### Example requires the pedmut package ###

if (requireNamespace("pedmut", quietly = TRUE)){

# A pedigree with 1 empty marker; attach 'equal' mutation model
x = nuclearPed(1) |>
  addMarker() |>
  setMutmod(model = "equal", rate = 0.01)

mutmod(x, 1)

# Update rate (but still "equal" model)
y = setMutmod(x, rate = 0.05, update = TRUE)
mutmod(y, 1)

# Change to stepwise model
z = setMutmod(x, model = "stepwise",
              rate = list(female = 0.01, male = 0.02),
              range = 0.1, rate2 = 1e-6)
mutmod(z, 1)

# Remove mutation model
w = setMutmod(x, model = NULL)
mutmod(w, 1)

}

pedtools documentation built on Nov. 5, 2023, 5:06 p.m.