hsphase (version 1.2.3)

hbp: Haplotype Blocks of Phased Data

Description

Creates a blocking structure matrix of the half-sib family based on phased data of the sire and half-sib family.

Usage

hbp(PhasedGenotypeMatrix, PhasedSireGenotype)

Arguments

PhasedGenotypeMatrix

matrix haplotypes for a half-sib family (two rows per individual)

PhasedSireGenotype

matrix haplotypes of sire

Value

• Returns a matrix where 3 or 4 stands for the SNP originating in, respectively, strands 1 and 2. 0 indicates that the source strand for the SNP is unknown.

See Also

aio, ssp

Examples

sire=matrix(c(
  0,0,0,0,0,1,                  # Haplotype one of the sire
  0,1,1,1,1,0                   # Haplotype two of the sire
  ), byrow=TRUE, ncol=6)
haplotypeHalfsib=matrix(c(
  1,0,1,1,1,1,                  # Individual one, haplotype one
  0,1,0,0,0,0,                  # Individual one, haplotype two
  0,1,1,0,1,1,                  # Individual two, haplotype one
  1,0,0,1,0,0                   # Individual two, haplotype two
  ), byrow=TRUE, ncol=6)        # 0s and 1s are alelle a and b
 hbp(haplotypeHalfsib, sire)