ts_mutate: Add mutations to the given tree sequence

In slendr: A Simulation Framework for Spatiotemporal Population Genetics

Add mutations to the given tree sequence

Description

Add mutations to the given tree sequence

Usage

ts_mutate(
  ts,
  mutation_rate,
  random_seed = NULL,
  keep_existing = TRUE,
  mut_type = NULL
)

Arguments

ts	Tree sequence object of the class slendr_ts
mutation_rate	Mutation rate used by msprime to simulate mutations
random_seed	Random seed passed to msprime's mutate method (if NULL, a seed will be generated between 0 and the maximum integer number available)
keep_existing	Keep existing mutations?
mut_type	Assign SLiM mutation type to neutral mutations? If NULL (default), no special mutation type will be used. If an integer number is given, mutations of the SLiM mutation type with that integer identifier will be created.

Value

Tree-sequence object of the class slendr_ts, which serves as an interface point for the Python module tskit using slendr functions with the ts_ prefix.

See Also

ts_nodes for extracting useful information about individuals, nodes, coalescent times and geospatial locations of nodes on a map

Examples

init_env()

# load an example model with an already simulated tree sequence
slendr_ts <- system.file("extdata/models/introgression_slim.trees", package = "slendr")
model <- read_model(path = system.file("extdata/models/introgression", package = "slendr"))

ts <- ts_load(slendr_ts, model)
ts_mutate <- ts_mutate(ts, mutation_rate = 1e-8, random_seed = 42)

ts_mutate

slendr documentation built on June 22, 2024, 6:56 p.m.