slendr (version 1.1.0)

ts_fst: 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
)

Value

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

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.

Examples

check_dependencies(python = TRUE, quit = TRUE) # dependencies must be present

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)

# 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")))