markerAxis: Compute chromosome breakpoints and tick positions

In diemr: Genome Polarization via Diagnostic Index Expectation Maximization

Compute chromosome breakpoints and tick positions

Description

Identifies chromosome breaks and calculates tick positions based on physical distances. Used for plotting genomic axes with consistent spacing.

Usage

markerAxis(includedSites, ChosenSites = "all", tickDist)

Arguments

includedSites	BED-like file defining genomic sites, ideally output from vcf2diem.
ChosenSites	Logical vector of sites to be analyzed.
tickDist	Distance between tick marks along the chromosome in bp.

Value

A list containing:

• CHROMbreaks: Positions of chromosome breaks.

• CHROMnamesPos: Midpoints for chromosome labels.

• CHROMnames: Unique chromosome names.

• ticksPos: Positions for tick marks.

• ticksNames: Tick labels in megabases.

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