aio: All-in-one Phasing

Description

Phasing of a half-sib family group.

Usage

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

Value

Returns a list of matrices. The first element (phasedHalfsibs) is a matrix with two rows (phased haplotypes) per individual (first paternal and second maternal). Data in format 0 (A), 1 (B) and 9 (unphased or missing). The second (sireHaplotype) and third (blockStructure) elements are the same as the output of ssp and bmh.

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)
bmh_forwardVectorSize: integer number of heterozygous sites used to validate recombination events or check for genotyping errors
bmh_excludeFP: logical excludes SNPs that may cause heterozygous sites in the sire due to genotyping errors or map errors
bmh_nsap: integer number of SNP per block to validate recombinations
output: character if equal to the phase the 'aio' will only return the phasing results

Details

This function calls the bmh, ssp and phf functions.

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