ts_fst: Calculate pairwise statistics between sets of individuals
In slendr: A Simulation Framework for Spatiotemporal Population Genetics

ts_fst

R Documentation

Calculate pairwise statistics between sets of individuals

Description

For a discussion on the difference between "site", "branch", and "node" options of the mode argument, please see the tskit documentation at https://tskit.dev/tskit/docs/stable/stats.html#sec-stats-mode.

Usage

ts_fst(
  ts,
  sample_sets,
  mode = c("site", "branch", "node"),
  windows = NULL,
  span_normalise = 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)
`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`) do not have to be specified as they are added automatically.
`span_normalise`	Divide the result by the span of the window? Default TRUE, see the tskit documentation for more detail.

Value

For each pairwise calculation, either a single Fst value or a vector of Fst values (one for each window)

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_load(slendr_ts, model) %>% ts_mutate(mutation_rate = 1e-8, random_seed = 42)

# compute F_st between two sets of individuals in a given tree sequence ts
ts_fst(ts, sample_sets = list(afr = c("AFR_1", "AFR_2", "AFR_3"),
                              eur = c("EUR_1", "EUR_2")))

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