GenoPop (version 1.0.0)

FixedSites: FixedSites

Description

This function counts the number of sites fixed for the alternative allele ("1") in a VCF file. It processes the file in two modes: the entire file at once or in specified windows across the genome. For batch processing, it uses process_vcf_in_batches. For windowed analysis, it uses a similar approach but tailored to process specific genomic windows (process_vcf_in_windows).

Usage

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

Value

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

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.

Details

The function has two modes of operation:

1. Batch Mode: Processes the entire VCF file in batches to count the total number of fixed sites for the alternative allele. Suitable for a general overview of the entire dataset.

2. Window Mode: Processes the VCF file in windows of a specified size and skip distance. This mode is useful for identifying regions with high numbers of fixed sites, which could indicate selective sweeps or regions of low recombination.

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_fixed_sites <- FixedSites(vcf_file)

# Window mode example
fixed_sites_df <- FixedSites(vcf_file, window_size = 100000, skip_size = 50000)