readIncludedSites: Read genomic sites from a BED-like file

In diemr: Genome Polarization via Diagnostic Index Expectation Maximization

Read genomic sites from a BED-like file

Description

Imports a BED-like file and optionally subsets sites.

Usage

readIncludedSites(includedSites, ChosenSites = "all")

Arguments

includedSites	Path to a BED-like file, ideally output from vcf2diem.
ChosenSites	Logical or numeric vector specifying sites to retain, or "all" to keep all sites.

Value

A data frame containing the selected sites with 1-based coordinates.

Examples

## Not run: 
# Run this example in a working directory with write permissions
myo <- system.file("extdata", "myotis.vcf", package = "diemr")
vcf2diem(myo, "myo")
readIncludedSites("myo-001.txt")
readIncludedSites("myo-001.txt", ChosenSites = 2:7)

## End(Not run)

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