OneDimSFS: OneDimSFS

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

OneDimSFS

Description

This function calculates a one-dimensional site frequency spectrum from a VCF file. It processes the file in batches for efficient memory usage. The user can decide between a folded or unfolded spectrum.

Usage

OneDimSFS(
  vcf_path,
  folded = FALSE,
  batch_size = 10000,
  threads = 1,
  write_log = FALSE,
  logfile = "log.txt",
  exclude_ind = NULL
)

Arguments

vcf_path	Path to the VCF file.
folded	Logical, deciding if folded (TRUE) or unfolded (FALSE) SFS is returned.
batch_size	The number of variants to be processed in each batch (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.
exclude_ind	Optional vector of individual IDs to exclude from the analysis. If provided, the function will remove these individuals from the genotype matrix before applying the custom function. Default is NULL, meaning no individuals are excluded.

Value

Site frequency spectrum as a named vector

Examples

vcf_file <- system.file("tests/testthat/sim.vcf.gz", package = "GenoPop")
index_file <- system.file("tests/testthat/sim.vcf.gz.tbi", package = "GenoPop")
sfs <- OneDimSFS(vcf_file, folded = FALSE)

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