coala (version 0.1.1)

feat_mutation: Feature: Mutation

Description

This functions adds the assumption to the model that neutral mutations occur in the genomes at a constant rate. The rate is quantified through a parameter usually named theta in population genetics. It equals 4*N0*mu, where N0 is the effective diploid population size of population one at the time of sampling and mu is the neutral mutation rate for an entire locus.

Usage

feat_mutation(rate, model = "IFS", base_frequencies = NA, tstv_ratio = NA,
  gtr_rates = NA)

Arguments

rate

A parameter defining the mutation rate.

model

The mutation model you want to use. Can be either 'IFS' (default), 'HKY' or 'GTR'. Refer to the mutation model section for detailed information.

base_frequencies

The equilibrium frequencies of the four bases used in the 'HKY' mutation model. Must be a numeric vector of length four, with the values for A, C, G and T, in that order.

tstv_ratio

The ratio of transitions to transversions used in the 'HKY' muation model.

gtr_rates

The rates for the six amino acid substitutions used in the 'GTR' model. Must be a numeric vector of length six. Order: A<->C, A<->G, A<->T, C<->G, C<->T, G<->T.

Value

• The feature, which can be added to a model using `+`.

Mutation Models

The Hasegawa, Kishino and Yano (HKY) model (Hasegawa et al., 1985) allows for a different rate of transitions and transversions (tstv_ratio) and unequal frequencies of the four nucleotides (base_frequencies).

The general reversible process (GTR) model (e.g. Yang, 1994) is more general than the HKY model and allows to define the rates for each type of substitution. The rates are assumed to be symmetric (e.g., the rate for T to G is equal to the one for G to T).

Examples

# A model with a constant mutation rate of 5:
model <- coal_model(10, 1) + feat_mutation(rate = 5)

# A model with a mutation rate that can be estimated with Jaatha:
model <- coal_model(c(15,20), 100) +
  feat_mutation(par_range('theta', 1, 20))