phf {hsphase}

Half-Sib Family Phasing

Description

Phases the half-sib family by using the blocking structure and imputed sire matrices.

Usage

phf(GenotypeMatrix, blockMatrix, sirePhasedMatrix)

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)

blockMatrix

matrix blocking structure (output of bmh)

sirePhasedMatrix

matrix imputed sire (output of ssp)

Value

Returns a matrix that contains the phased parental haplotypes of the half-sibs. It uses 1, 0 and 9 for A, B and missing.

Note

The genotype matrix must only contain individuals from one half-sib family and one ordered chromosome. This function is used by the aio function for complete phasing of a half-sib group.

See Also

aio

Examples

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