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diemr (version 1.4.3)

Diagnostic Index Expectation Maximisation in R

Description

Likelihood-based genome polarisation finds which alleles of genomic markers belong to which side of the barrier. Co-estimates which individuals belong to either side of the barrier and barrier strength. Uses expectation maximisation in likelihood framework. The method is described in Baird et al. (2023) .

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Version

Install

install.packages('diemr')

Monthly Downloads

248

Version

1.4.3

License

GPL (>= 3)

Maintainer

Natalia Martinkova

Last Published

January 20th, 2025

Functions in diemr (1.4.3)

truncatedLaplace

Truncated Laplace distribution to 95% of area under the curve, weights scaled to 10/19

unbiasedWeightedStateChoice

Selects weighted mode of the genomic state

Convert vcf files to diem format

Dataset of Fish Genotypes

Plot Polarized Genotypes

Add a Marker Axis with Chromosome Names to a Plot of Polarized Genotypes

Polarises a marker

CheckDiemFormat

diem input file checker

ModelOfDiagnostic

Model of Diagnostic Marker Based on All Individual State Counts

importPolarized

Imports genomic data polarized according to the specification

pHetErrOnStateCount

Hybrid index, heterozygosity, error rate

Plot the De Finetti Diagram for Polarized Genotypes

Dataset of Modified Genotypes of Bats

Diagnostic Index Expectation Maximisation

Dataset of Butterfly Genotypes

Count states in a vector

smoothPolarizedGenotypes

Smooth Polarized Genotype States

Convert SNP Ranks To Windows Corresponding to Mapping Distance