aio: 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")

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

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.

Examples

Run this code

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