Compute Tajima's D for a sliding window — windows_pop_tajimas

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