windows_pop_tajimas_d: 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
)

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

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.

Examples

Run this code

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
  )

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