ts_afs: Compute the allele frequency spectrum (AFS)

In bodkan/spannr: A Simulation Framework for Spatiotemporal Population Genetics

Compute the allele frequency spectrum (AFS)

Description

This function computes the AFS with respect to the given set of individuals or nodes.

Usage

ts_afs(
  ts,
  sample_sets = NULL,
  mode = c("site", "branch", "node"),
  windows = NULL,
  span_normalise = FALSE,
  polarised = TRUE
)

Arguments

ts	Tree sequence object of the class slendr_ts
sample_sets	A list (optionally a named list) of character vectors with individual names (one vector per set). If NULL, allele frequency spectrum for all individuals in the tree sequence will be computed.
mode	The mode for the calculation ("sites" or "branch")
windows	Coordinates of breakpoints between windows. The first coordinate (0) and the last coordinate (equal to ts$sequence_length) are added automatically)
span_normalise	Argument passed to tskit's allele_frequency_spectrum method
polarised	When TRUE (the default) the allele frequency spectrum will not be folded (i.e. the counts will assume knowledge of which allele is ancestral, and which is derived, which is known in a simulation)

Details

For more information on the format of the result and dimensions, in particular the interpretation of the first and the last element of the AFS (when complete = TRUE), please see the tskit manual at https://tskit.dev/tskit/docs/stable/python-api.html and the example section dedicated to AFS at https://tskit.dev/tutorials/analysing_tree_sequences.html#allele-frequency-spectra.

Value

Allele frequency spectrum values for the given sample set. Note that the contents of the first and last elements of the AFS might surprise you. Read the links in the description for more detail on how tskit handles things.

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"))

# load the tree-sequence object from disk
ts <- ts_read(slendr_ts, model) %>% ts_mutate(mutation_rate = 1e-8, random_seed = 42)

samples <- ts_samples(ts) %>% .[.$pop %in% c("AFR", "EUR"), ]

# compute AFS for the given set of individuals
ts_afs(ts, sample_sets = list(samples$name))

bodkan/spannr documentation built on Dec. 19, 2024, 11:43 p.m.