impute {hsphase}

Impute of Low Density SNP Marker to High Density (Paternal Strand)

Description

Impute the paternal strand from low density to high density utilising high density sire haplotype.

Usage

impute(halfsib_genotype_ld, sire_hd, bmh_forwardVectorSize = 30, 
bmh_excludeFP = TRUE, bmh_nsap = 3)

Arguments

halfsib_genotype_ld

matrix half-sib genotypes with low density marker (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)

sire_hd

matrix haplotype of sire (this parameter can be sequence data or any phased sire - the matrix should have rownames which are the sample IDs and colnames which are the SNP names)

bmh_forwardVectorSize

integer number of heterozygous sites used to validate recombination events or check for genotyping errors

bmh_excludeFP

logical exclude SNPs that may cause heterozygous sites in the sire due to genotyping errors or map errors

bmh_nsap

integer number of SNPs per block

Value

Return an imputed half-sib matrix.

See Also

bmh, ssp and phf