Estimate window statistics from per locus estimates — windows_stats

This function is mostly designed for developers: it is a general function to estimate window statistics from per locus estimates. This function takes a vector of per locus estimates, and aggregates them by sum or mean per window. To compute specific quantities directly from a gen_tibble, use the appropriate window_* functions, e.g windows_pairwise_pop_fst() to compute pairwise Fst.

Usage

windows_stats_generic(
  .x,
  loci_table,
  operator = c("mean", "sum", "custom"),
  window_size,
  step_size,
  size_unit = c("snp", "bp"),
  min_loci = 1,
  complete = FALSE,
  f = NULL,
  ...
)

Arguments

.x: A vector containing the per locus estimates.
loci_table: a dataframe including at least a column 'chromosome', and additionally a column 'position' if size_unit is "bp".
operator: The operator to use for the window statistics. Either "mean", "sum" or "custom" to use a custom function .f.
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.
f: a custom function to use for the window statistics. This function should take a vector of locus estimates and return a single value.
...: Additional arguments to be passed to the custom operator function.

Value

A tibble with columns: 'chromosome', 'start', 'end', 'stats', and 'n_loci'. The 'stats' column contains the mean of the per locus estimates in the window, and 'n_loci' contains the number of loci in the window.