aio: All-in-one Phasing

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

All-in-one Phasing

Description

Phasing of a single half-sib family group (single ordered chromosome).

Usage

aio(genotypeMatrix, bmh_forwardVectorSize = 30, bmh_excludeFP = TRUE,
    bmh_nsap = 3, bmh_fillMissing = FALSE, output = "phase")

Arguments

genotypeMatrix	matrix. Half-sib genotypes (one half-sib per row, SNPs ordered by map position in columns). Data must be numeric: 0, 1, 2 for AA, AB, BB. Use 9 for missing.
bmh_forwardVectorSize	integer. Number of heterozygous sites used to validate recombination events or detect genotyping/map errors.
bmh_excludeFP	logical. Exclude SNPs that may induce false heterozygous sites in the sire due to genotyping or map errors.
bmh_nsap	integer. Number of SNP per block to validate recombinations (e.g. 50K \to 3, 700K \to 10).
bmh_fillMissing	logical. If TRUE, recombination points are placed at the mid-point of the ambiguous interval rather than marking surrounding SNPs as missing.
output	character. If "phase", the function returns only the phased haplotypes matrix.

Details

This function calls bmh, ssp, and phf.

Value

If output = "phase", returns a haplotype matrix with two rows per individual (first paternal, second maternal), coded as 0 (allele A), 1 (allele B), and 9 (missing/unphased).

Otherwise returns a list with elements:

• phasedHalfsibs

• sireHaplotype

• blockStructure

Note

Only this function needs to be called to phase a half-sib family. The genotype matrix must contain individuals from a single family and a single ordered chromosome.

See Also

bmh, ssp, phf

Examples

genotype <- matrix(c(       # Define a Half-sib Genotype Matrix
  2,1,0,	            # Individual 1
  2,0,0,                    # Individual 2
  0,0,2                     # Individual 3
), byrow = TRUE, ncol = 3)  # There are 3 individulas with three SNPs

aio(genotype)               # The genotypes must include only one half-sib family and one chromosome

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