SingletonSites: SingletonSites

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

SingletonSites

Description

This function counts the number of singleton sites (sites where a minor allele occurs only once in the sample) in a VCF file. It processes the file in batches or specified windows across the genome. 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

SingletonSites(
  vcf_path,
  threads = 1,
  write_log = FALSE,
  logfile = "log.txt",
  batch_size = 10000,
  window_size = NULL,
  skip_size = NULL,
  exclude_ind = NULL
)

Arguments

vcf_path	Path to the VCF file.
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.
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).
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.
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

In batch mode (no window_size or skip_size provided): A single integer representing the total number of singleton sites across the entire VCF file. In window mode (window_size and skip_size provided): A data frame with columns 'Chromosome', 'Start', 'End', and 'SingletonSites', representing the count of singleton sites within each window.

Examples

# Batch mode example
vcf_file <- system.file("tests/testthat/sim.vcf.gz", package = "GenoPop")
index_file <- system.file("tests/testthat/sim.vcf.gz.tbi", package = "GenoPop")
num_singleton_sites <- SingletonSites(vcf_file)

# Window mode example
vcf_path <- "path/to/vcf/file"
singleton_sites_df <- SingletonSites(vcf_file, window_size = 100000, skip_size = 50000)

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