calculate_fst: Calculate Fixation Index (Fst)

In surh/HMVAR: Human Microbiome Variant Analysis in R

Description

Calculates Fst from imported midas data

Usage

calculate_fst(
  Dat,
  map,
  method = "Weir-Cockerham",
  support_thres = 1,
  w_size = NULL,
  s_size = NULL,
  sorted = FALSE,
  verbose = TRUE
)

Arguments

Dat	A MIDAS dataset. Imported into R with read_midas_data
map	A tibble with columns sample and Group corresponding to sample names in MIDAS dataset and sample population respectiveley.
method	Weir-Cockerham or Fstpool.
support_thres	calculate_fst uses the depth slot of the MIDAS data as a 'support' value to decide if a site in a given sample will be considered. If it corresponds to depth, this is the minimum coverage at a site at a given sample.
w_size	Window size in bp. If both w_size and s_size are numeric. Fst/Fst^pool values are calculated for a sliding window.
s_size	Window step size in bp. If both w_size and s_size are numeric. Fst/Fst^pool values are calculated for a sliding window.
sorted	Logical indicating if sites are sorted in ascending orderby ref_pos within each ref_id. Only used if sliding windows are calculated
verbose	Logical indicating if progress during site level calculations must be printed.

Value

A list with tibbles fst and w_fst corresponding to site and window level Fst calculations. w_fst is NULL if no window calculations are performed.

surh/HMVAR documentation built on Aug. 18, 2021, 1:21 a.m.