ohd: Opposing Homozygote Detection

In hsphase: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data

Opposing Homozygote Detection

Description

Counts, for each animal, the number of loci where it contributes opposing homozygotes in sites that imply heterozygosity in the sire.

Usage

ohd(genotypeMatrix, unique_check = FALSE, SNPs = 6000)

Arguments

genotypeMatrix	matrix. Half-sib genotypes (one half-sib per row, SNPs ordered by mapping position in the columns). Data should be numeric: 0, 1, 2 for AA, AB, BB and 9 for missing.
unique_check	logical. If TRUE, counts opposing homozygotes using a uniqueness rule (see Details).
SNPs	integer. Number of SNPs to use. (Only applicable if supported by the installed version.)

Value

A numeric vector with the number of heterozygous sites that each sample caused.

Note

This function can be used to identify pedigree errors; i.e., outliers with unusually high values.

Author(s)

This method was suggested by Bruce Tier <[e-mail]> to identify pedigree errors.

Examples

genotype <- matrix(c(
  2,1,0,
  2,0,0,
  0,0,2
), byrow = TRUE, ncol = 3)

ohd(genotype)

hsphase documentation built on Feb. 17, 2026, 5:07 p.m.