windows_pop_tajimas_d: Compute Tajima's D for a sliding window

In tidypopgen: Tidy Population Genetics

Compute Tajima's D for a sliding window

Description

This function computes Tajima's D for a sliding window across each chromosome.

Usage

windows_pop_tajimas_d(
  .x,
  type = c("matrix", "tidy", "list"),
  window_size,
  step_size,
  size_unit = c("snp", "bp"),
  min_loci = 1,
  complete = FALSE
)

Arguments

.x	a (potentially grouped) gen_tibble object
type	type of object to return, if using grouped method. One of "matrix", "tidy", or "list". Default is "matrix".
window_size	The size of the window to use for the estimates.
step_size	The step size to use for the windows.
size_unit	Either "snp" or "bp". If "snp", the window size and step size are in number of SNPs. If "bp", the window size and step size are in base pairs.
min_loci	The minimum number of loci required to calculate a window statistic. If the number of loci in a window is less than this, the window statistic will be NA.
complete	Should the function be evaluated on complete windows only? If FALSE, the default, then partial computations will be allowed at the end of the chromosome.

Value

if data is not grouped, a data frame with the following columns:

• chromosome: the chromosome for the window

• start: the starting locus of the window

• end: the ending locus of the window

• tajimas_d: the Tajima's D for the population if data are grouped, either: a data frame as above with the following columns:

• chromosome: the chromosome for the window

• start: the starting locus of the window

• end: the ending locus of the window

• n_loci: the number of loci in the window

• group: the Tajima's D for the group for the given window (there will be as many of these columns as groups in the gen_tibble, and they will be named by the grouping levels) a tidy tibble with the following columns:

• chromosome: the chromosome for the window

• start: the starting locus of the window

• end: the ending locus of the window

• n_loci: the number of loci in the window

• group: the name of the group

• stat: the Tajima's D for the given group at the given window or a list of data frames, one per group, with the following columns:

• chromosome: the chromosome for the window

• start: the starting locus of the window

• end: the ending locus of the window

• stat: the Tajima's D for the given window

• n_loci: the number of loci in the window

Examples

example_gt <- load_example_gt("grouped_gen_tbl")

# Calculate Tajima's D across a window of 3 SNPs, with a step size of 2 SNPs
example_gt %>%
  windows_pop_tajimas_d(
    window_size = 3, step_size = 2,
    size_unit = "snp", min_loci = 2
  )

tidypopgen documentation built on Aug. 28, 2025, 1:08 a.m.