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Calculate the f2, f3, f4, and f4-ratio statistics

Source: R/tree-sequences.R
ts_f4ratio.Rd

These functions present an R interface to the corresponding f-statistics methods in tskit.

Usage

ts_f2(
  ts,
  A,
  B,
  mode = c("site", "branch", "node"),
  span_normalise = TRUE,
  windows = NULL
)

ts_f3(
  ts,
  A,
  B,
  C,
  mode = c("site", "branch", "node"),
  span_normalise = TRUE,
  windows = NULL
)

ts_f4(
  ts,
  W,
  X,
  Y,
  Z,
  mode = c("site", "branch", "node"),
  span_normalise = TRUE,
  windows = NULL
)

ts_f4ratio(
  ts,
  X,
  A,
  B,
  C,
  O,
  mode = c("site", "branch"),
  span_normalise = TRUE
)

Arguments

ts

Tree sequence object of the class slendr_ts

mode

The mode for the calculation ("sites" or "branch")

span_normalise

Divide the result by the span of the window? Default TRUE, see the tskit documentation for more detail.

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.

W, X, Y, Z, A, B, C, O

Character vectors of individual names (largely following the nomenclature of Patterson 2021, but see crucial differences between tskit and ADMIXTOOLS in Details)

Value

Data frame with statistics calculated for the given sets of individuals

Details

Note that the order of populations f3 statistic implemented in tskit (https://tskit.dev/tskit/docs/stable/python-api.html#tskit.TreeSequence.f3) is different from what you might expect from ADMIXTOOLS, as defined in Patterson 2012 (see doi:10.1534/genetics.112.145037 under heading "The three-population test and introduction of f-statistics", as well as ADMIXTOOLS documentation at https://github.com/DReichLab/AdmixTools/blob/master/README.3PopTest#L5). Specifically, the widely used notation introduced by Patterson assumes the population triplet as f3(C; A, B), with C being the "focal" sample (i.e., either the outgroup or a sample tested for admixture). In contrast, tskit implements f3(A; B, C), with the "focal sample" being A.

Although this is likely to confuse many ADMIXTOOLS users, slendr does not have much choice in this, because its ts_*() functions are designed to be broadly compatible with raw tskit methods.

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 and add mutations to it
ts <- ts_read(slendr_ts, model) %>% ts_mutate(mutation_rate = 1e-8, random_seed = 42)

# calculate f2 for two individuals in a previously loaded tree sequence
ts_f2(ts, A = "AFR_1", B = "EUR_1")
#> # A tibble: 1 × 3
#>   A     B           f2
#>   <chr> <chr>    <dbl>
#> 1 AFR_1 EUR_1 0.000028

# calculate f2 for two sets of individuals
ts_f2(ts, A = c("AFR_1", "AFR_2"), B = c("EUR_1", "EUR_3"))
#> # A tibble: 1 × 3
#>   A           B                  f2
#>   <chr>       <chr>           <dbl>
#> 1 AFR_1+AFR_2 EUR_1+EUR_3 0.0000307

# calculate f3 for two individuals in a previously loaded tree sequence
ts_f3(ts, A = "EUR_1", B = "AFR_1", C = "NEA_1")
#> # A tibble: 1 × 4
#>   A     B     C            f3
#>   <chr> <chr> <chr>     <dbl>
#> 1 EUR_1 AFR_1 NEA_1 -0.000019

# calculate f3 for two sets of individuals
ts_f3(ts, A = c("AFR_1", "AFR_2", "EUR_1", "EUR_2"),
          B = c("NEA_1", "NEA_2"),
          C = "CH_1")
#> # A tibble: 1 × 4
#>   A                       B           C           f3
#>   <chr>                   <chr>       <chr>    <dbl>
#> 1 AFR_1+AFR_2+EUR_1+EUR_2 NEA_1+NEA_2 CH_1  0.000157

# calculate f4 for single individuals
ts_f4(ts, W = "EUR_1", X = "AFR_1", Y = "NEA_1", Z = "CH_1")
#> # A tibble: 1 × 5
#>   W     X     Y     Z           f4
#>   <chr> <chr> <chr> <chr>    <dbl>
#> 1 EUR_1 AFR_1 NEA_1 CH_1  0.000011

# calculate f4 for sets of individuals
ts_f4(ts, W = c("EUR_1", "EUR_2"),
          X = c("AFR_1", "AFR_2"),
          Y = "NEA_1",
          Z = "CH_1")
#> # A tibble: 1 × 5
#>   W           X           Y     Z            f4
#>   <chr>       <chr>       <chr> <chr>     <dbl>
#> 1 EUR_1+EUR_2 AFR_1+AFR_2 NEA_1 CH_1  0.0000205

# calculate f4-ratio for a given set of target individuals X
ts_f4ratio(ts, X = c("EUR_1", "EUR_2", "EUR_4", "EUR_5"),
               A = "NEA_1", B = "NEA_2", C = "AFR_1", O = "CH_1")
#> # A tibble: 4 × 6
#>   X     A     B     C     O      alpha
#>   <chr> <chr> <chr> <chr> <chr>  <dbl>
#> 1 EUR_1 NEA_1 NEA_2 AFR_1 CH_1  0.0625
#> 2 EUR_2 NEA_1 NEA_2 AFR_1 CH_1  0.170 
#> 3 EUR_4 NEA_1 NEA_2 AFR_1 CH_1  0.0455
#> 4 EUR_5 NEA_1 NEA_2 AFR_1 CH_1  0