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 the number of opposing homozygotes for each animal that caused a heterozygus site in the sire.

Usage

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

Arguments

genotypeMatrix	matrix half-sib genotypes (one half-sib per row, with SNP ordered by mapping position in the columns. Data should be numeric. Use 0, 1 and 2 respectively for AA, AB and BB. Use 9 for missing data)
unique_check	logical check if samples uniquely originate an opposing homozygote at a locus
SNPs	integer number of SNP to use

Value

Returns a vector with the number of heterozygous sites that each sample caused.

Note

This function can be used to identify pedigree errors; i.e., the outliers.

Author(s)

This method is 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 May 29, 2024, 2:20 a.m.