check_trio: Check markers for parent-offspring trio

In jendelman/polyBreedR: Genomics-assisted breeding for polyploids (and diploids)

Check markers for parent-offspring trio

Description

Check markers for parent-offspring trio

Usage

check_trio(parentage, geno, ploidy)

Arguments

parentage	Data frame with three columns: id, mother, father
geno	Matrix of allele dosages: markers x indiv
ploidy	2 or 4

Details

Computes the percentage of markers at which the two parents and offspring have incompatible allele dosages (for tetraploids, the random bivalents model is used). For dihaploid offspring of a single tetraploid parent, use ploidy = 4 and "haploid" for the father in parentage, as well as a diploid (0,1,2) genotype for the offspring. A small amount of missing genotype data can be tolerated.

Value

Data frame with the percentage of incompatible markers for each trio

jendelman/polyBreedR documentation built on Jan. 5, 2025, 12:13 a.m.