Fst: Fst

In GenoPop: Genotype Imputation and Population Genomics Efficiently from Variant Call Formatted (VCF) Files

Fst

Description

This function calculates the fixation index (Fst) between two populations from a VCF file using the method of Weir and Cockerham (1984). The formula used for this is equivalent to the one used in vcftools –weir-fst-pop (https://vcftools.sourceforge.net/man_latest.html). For batch processing, it uses process_vcf_in_batches. For windowed analysis, it uses a similar approach tailored to process specific genomic windows (process_vcf_in_windows).

Usage

Fst(
  vcf_path,
  pop1_individuals,
  pop2_individuals,
  weighted = FALSE,
  batch_size = 10000,
  threads = 1,
  write_log = FALSE,
  logfile = "log.txt",
  window_size = NULL,
  skip_size = NULL
)

Arguments

vcf_path	Path to the VCF file.
pop1_individuals	Vector of individual names belonging to the first population.
pop2_individuals	Vector of individual names belonging to the second population.
weighted	Logical, whether weighted Fst or mean Fst is returned (Default = FALSE (mean Fst is returned)).
batch_size	The number of variants to be processed in each batch (used in batch mode only, default of 10,000 should be suitable for most use cases).
threads	Number of threads to use for parallel processing.
write_log	Logical, indicating whether to write progress logs.
logfile	Path to the log file where progress will be logged.
window_size	Size of the window for windowed analysis in base pairs (optional). When specified, skip_size must also be provided.
skip_size	Number of base pairs to skip between windows (optional). Used in conjunction with window_size for windowed analysis.

Value

In batch mode (no window_size or skip_size provided): Fst value (either mean or weighted). In window mode (window_size and skip_size provided): A data frame with columns 'Chromosome', 'Start', 'End', and 'Fst', representing the fixation index within each window.

Examples

vcf_file <- system.file("tests/testthat/sim.vcf.gz", package = "GenoPop")
index_file <- system.file("tests/testthat/sim.vcf.gz.tbi", package = "GenoPop")
pop1_individuals <- c("tsk_0", "tsk_1", "tsk_2")
pop2_individuals <- c("tsk_3", "tsk_4", "tsk_5")
# Batch mode example
fst_value <- Fst(vcf_file, pop1_individuals, pop2_individuals, weighted = TRUE)
# Window mode example
fst_windows <- Fst(vcf_file, pop1_individuals, pop2_individuals, weighted = TRUE,
                   window_size = 100000, skip_size = 50000)

GenoPop documentation built on April 3, 2025, 9:51 p.m.