ohg: Matrix of Opposing Homozygotes

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

Matrix of Opposing Homozygotes

Description

Creates a matrix of opposing homozygotes from the genotype matrix.

Usage

ohg(genotypeMatrix)

Arguments

genotypeMatrix

matrix genotype (Data should be numeric. Use 0, 1 and 2 respectively for AA, AB and BB. Use 9 for missing data)

Value

Returns a square matrix (sample X sample) with the pairwise counts of opposing homozygotes.

Note

This function can be slow with a large data set. The fast version of this function will be available after publish of the related manuscript.

Author(s)

Ferdosi, M. H., & Boerner, V. (2014). A fast method for evaluating opposing homozygosity in large SNP data sets. Livestock Science.

See Also

rpoh

Examples

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

hsphase documentation built on May 29, 2024, 2:20 a.m.