rank2mapChr

Determines the start and end positions of SNPs within a sliding window along a chromosome.
Uses a two-pointer approach for efficiency.

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

rank2mapChr function

<dl><dt>x</dt>
<dd>A numeric vector of sorted SNP positions.</dd>
<dt>windowSize</dt>
<dd>The size of the genomic window in base pairs.</dd></dl>

Arguments

Map SNP positions to ranks within a genomic window — rank2mapChr

<dl>

<dt>x</dt>
<dd>A numeric vector of sorted SNP positions.</dd>


<dt>windowSize</dt>
<dd>The size of the genomic window in base pairs.</dd>

</dl>

rank2mapChr: Map SNP positions to ranks within a genomic window

Description

Usage

Value

Arguments

Details