impute: Impute of Low Density SNP Marker to High Density (Paternal...
In hsphase: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data

impute

R Documentation

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

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

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

`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

Return an imputed half-sib matrix.