Calculate pairwise statistics between sets of individualsSource:
For a discussion on the difference between "site", "branch", and "node"
options of the
mode argument, please see the tskit documentation at
ts_fst( ts, sample_sets, mode = c("site", "branch", "node"), windows = NULL, span_normalise = TRUE )
Tree sequence object of the class
A list (optionally a named list) of character vectors with individual names (one vector per set)
The mode for the calculation ("sites" or "branch")
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.
Divide the result by the span of the window? Default TRUE, see the tskit documentation for more detail.
For each pairwise calculation, either a single Fst value or a vector of Fst values (one for each window)
check_dependencies(python = TRUE) # make sure dependencies are 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.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, mutate = TRUE, 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 0.933