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 half-sib family group.

Usage

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

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.

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.

Note

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

See Also

bmh, ssp and 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 May 29, 2024, 2:20 a.m.