Genome Polarization via Diagnostic Index Expectation Maximization
Dataset of Butterfly Genotypes
diem input file checker
Diagnostic Index Expectation Maximisation
Polarises a marker
Compute hybrid index from genotypes, file, or numeric vector
Imports genomic data polarized according to the specification
Compute chromosome breakpoints and tick positions
Model of Diagnostic Marker Based on All Individual State Counts
Dataset of Modified Genotypes of Bats
Hybrid index, heterozygosity, error rate
Plot the De Finetti Diagram for Polarized Genotypes
Add a Marker Axis with Chromosome Names to a Plot of Polarized Genotyp...
Plot Polarized Genotypes
Convert SNP Ranks To Windows Corresponding to Mapping Distance
Map SNP positions to ranks within a genomic window
Read genomic sites from a BED-like file
Resolve compartments for diem input files
Import a single diem-formatted genotype file
Smooth Polarized Genotype States
Count states in a vector
Dataset of Fish Genotypes
Compute truncated Laplace distribution weights
Select the weighted mode of genomic states
Identify Variant Sites in Genotype Files
Convert vcf files to diem format
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>.
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