markerAxis

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

internal

Implements a likelihood-based method for genome polarization, identifying
which alleles of SNV markers belong to either side of a barrier to gene flow. The
approach co-estimates individual assignment, barrier strength, and divergence between
sides, with direct application to studies of hybridization. Includes VCF-to-diem
conversion and input checks, support for mixed ploidy and parallelization, and tools
for visualization and diagnostic outputs. Based on diagnostic index expectation
maximization as described in Baird et al. (2023) <doi:10.1111/2041-210X.14010>.

Natalia Martinkova

diemr

Genome Polarization via Diagnostic Index Expectation
Maximization

Stuart Baird

markerAxis function

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

Arguments

Compute chromosome breakpoints and tick positions — markerAxis

<dl>

<dt>includedSites</dt>
<dd>BED-like file defining genomic sites, ideally output from <code>vcf2diem</code>.</dd>


<dt>ChosenSites</dt>
<dd>Logical vector of sites to be analyzed.</dd>


<dt>tickDist</dt>
<dd>Distance between tick marks along the chromosome in bp.</dd>

</dl>

markerAxis: Compute chromosome breakpoints and tick positions

Description

Usage

Value

Arguments