View source: R/feature_mutation.R
feat_mutation  R Documentation 
This feature adds mutations to a model. Mutations occur in the genomes
of the individuals with a given rate
. The rate is per locus
for unlinked loci and per trio for linked
locus trios. By default, the same mutation rate is used
for all loci, but it is possible to change this with par_variation
and par_zero_inflation
.
feat_mutation(
rate,
model = "IFS",
base_frequencies = NA,
tstv_ratio = NA,
gtr_rates = NA,
fixed_number = FALSE,
locus_group = "all"
)
rate 
The mutation rate. Can be a numeric or a 
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. 
fixed_number 
If set to 
locus_group 
The loci for which this features is used. Can either be

The feature, which can be added to a model using +
.
The feature, which can be added to a model created with
coal_model
using +
.
The infinite sites mutation (IFS) model is a frequently used simplification in population genetics. It assumes that each locus consists of infinitely many sites at which mutations can occur, and each mutation hits a new site. Consequently, there are no backmutations with this model. It does not generate DNA sequences, but rather only 0/1 coded data, were 0 denotes the ancestral state of the site, and 1 the derived state created by a mutation.
The other mutation models are finite site models that generate more realistic sequences.
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).
For using rates that variate between the loci in a model:
par_variation
, par_zero_inflation
For adding recombination: feat_recombination
.
For creating a model: coal_model
Other features:
feat_growth()
,
feat_ignore_singletons()
,
feat_migration()
,
feat_outgroup()
,
feat_pop_merge()
,
feat_recombination()
,
feat_selection()
,
feat_size_change()
,
feat_unphased()
# A model with a constant mutation rate of 5:
model < coal_model(5, 1) + feat_mutation(5) + sumstat_seg_sites()
simulate(model)
# A model with a mutation of 5.0 for the first 10 loci, and 7.5 for the
# second 10 loci
model < coal_model(4) +
locus_averaged(10, 100) +
locus_averaged(10, 100) +
feat_mutation(5.0, locus_group = 1) +
feat_mutation(7.5, locus_group = 2) +
sumstat_seg_sites()
simulate(model)
# A model with 7 mutations per locus:
model < coal_model(5, 1) +
feat_mutation(7, fixed = TRUE) +
sumstat_seg_sites()
simulate(model)
# A model using the HKY model:
model < coal_model(c(10, 1), 2) +
feat_mutation(7.5, model = "HKY", tstv_ratio = 2,
base_frequencies = c(.25, .25, .25, .25)) +
feat_outgroup(2) +
feat_pop_merge(1.0, 2, 1) +
sumstat_seg_sites()
## Not run: simulate(model)
# A model using the GTR model:
model < coal_model(c(10, 1), 1, 25) +
feat_mutation(7.5, model = "GTR",
gtr_rates = c(1, 1, 1, 1, 1, 1) / 6) +
feat_outgroup(2) +
feat_pop_merge(1.0, 2, 1) +
sumstat_dna()
## Not run: simulate(model)$dna
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