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
check_dependencies(python = TRUE, quit = TRUE) # dependencies must be present
init_env()
#> The interface to all required Python modules has been activated.
# 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")))
#> # A tibble: 1 × 3
#> x y Fst
#> <chr> <chr> <dbl>
#> 1 afr eur 0.324