mutationModel: Mutation models

In magnusdv/pedmut: Mutation Models for Pedigree Likelihood Computations

Mutation models

Description

Constructor for the class mutationModel. An object of this class is essentially a list of two mutation matrices, named "female" and "male".

Usage

mutationModel(
  model,
  alleles = NULL,
  afreq = NULL,
  matrix = NULL,
  rate = NULL,
  rate2 = NULL,
  range = NULL,
  seed = NULL,
  validate = TRUE
)

validateMutationModel(mutmod, alleles = NULL)

sexEqual(mutmod)

Arguments

model	Either: a mutationModel object (returned unchanged after validation) a single mutationMatrix object (will be applied to both genders) a list of two mutationMatrix objects, named "female" and "male" a single model name (see mutationMatrix() for valid options) a list of two model names, named "female" and "male"
alleles	A character vector with allele labels; passed on to mutationMatrix().
afreq	A numeric vector of allele frequencies; passed on to mutationMatrix().
matrix	A matrix, or a list of two (named "female" and "male")
rate	A numeric mutation rate, or a list of two (named "female" and "male")
rate2	A numeric mutation rate, or a list of two (named "female" and "male"). Required in the "stepwise" model; see mutationMatrix() for details.
range	A positive number, or a list of two (named "female" and "male"). Required in the "stepwise" model; see mutationMatrix() for details.
seed	An integer, or a list of two (named "female" and "male").
validate	A logical, by default TRUE.
mutmod	A mutationModel object.

Value

An object of class mutationModel. This is a list of two mutationMatrix objects, named "female" and "male", and the following attributes:

• sexEqual : TRUE if both genders have identical models, otherwise FALSE

• alwaysLumpable : TRUE if both genders have models that are lumpable for any allele subset, otherwise FALSE

Examples

# "Equal" model, same parameters for both genders
M1 = mutationModel("eq", alleles = 1:2, rate = 0.1)
M1

# Different mutation rates
M2 = mutationModel("eq", alleles = 1:2, rate = list(male = 0.1, female = 0.01))
M2

stopifnot(identical(M1$male, M1$female), identical(M2$male, M1$male))

# A custom mutation matrix:
mat = matrix(c(0,0,1,1), ncol = 2, dimnames = list(1:2, 1:2))
M3 = mutationModel(model = "custom", matrix = mat)

# Under the hood arguments are passed to `mutationMatrix()`.
# Alternatively, this can be done explicitly in the `model` argument
M4 = mutationModel(model = mutationMatrix("custom", matrix = mat))

stopifnot(identical(M3, M4))

# The latter strategy is needed e.g. in pedtools::marker(), which gives the
# user access to `model`, but not `matrix`.

magnusdv/pedmut documentation built on Jan. 31, 2024, 7:06 a.m.