variantSites: Identify Variant Sites in Genotype Files

In diemr: Genome Polarization via Diagnostic Index Expectation Maximization

Identify Variant Sites in Genotype Files

Description

This function processes genotype data from multiple files to identify variant markers based on homozygosity thresholds for a set of individuals. It supports parallel processing to improve performance when handling large datasets.

Usage

variantSites(
  files,
  filename = "variantSites.txt",
  ChosenInds = "all",
  requireHomozygous = TRUE,
  nCores = 1
)

Arguments

files	A character vector with paths to files with genotypes.
filename	A character vector with a path where to save the converted genotypes.
ChosenInds	A numeric or logical vector of indices of individuals to be included in the analysis.
requireHomozygous	A logical or numeric vector indicating whether to require the site to have at least one or more homozygous individual(s) for each allele.
nCores	A numeric number of cores to be used for parallelisation. Must be nCores = 1 on Windows.

Details

The results are written to a specified output file and also returned as a logical vector.

A marker is considered a variant if at least requireHomozygous individuals are homozygous for each of the two alleles encoded in the diem-formatted input files.

Parallel processing when nCores > 1 is available only for non-Windows operation Windows computers must use nCores = 1. systems.

Value

A logical vector indicating whether each marker in the dataset is a variant site (TRUE) or not (FALSE). The same results are also written to the specified output file.

Examples

# Run this example in a folder with write permission
files <- c(
  system.file("extdata", "data7x3.txt", package = "diemr"),
  system.file("extdata", "data7x10.txt", package = "diemr")
)
## Not run: 

variant1 <- variantSites(files, filename = "v1.txt")
variant2 <- variantSites(files, filename = "v2.txt", requireHomozygous = 2)

## End(Not run)

diemr documentation built on Dec. 11, 2025, 5:07 p.m.