ssp: Sire Imputation and Phasing

In hsphase: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data

Description

Infer (impute) and phase sire's genotype based on the block structure matrix (recombination blocks) and homozygous sites of the half-sib genotype matrix.

Usage

ssp(blockMatrix, genotypeMatrix)

Arguments

blockMatrix	matrix block structure (Output of bmh)
genotypeMatrix	matrix half-sibs genotype (each row includes the SNP of individuals, 0, 1 and 2 for respectively AA, AB and BB. Use 9 for missing data)

Value

Returns a matrix (Imputed Sire) with two rows one for each haplotype of the sire (columns are SNP in the order of the genotype matrix). Alleles are coded as 0 (A) and 1 (B). Alleles that could not be imputed are coded as 9.

See Also

phf, aio and imageplot

Examples

genotype <- matrix(c(
0,2,1,1,1,
2,0,1,2,2,
2,2,1,0,2,
2,2,1,1,1,
0,0,2,1,0), ncol = 5, byrow = TRUE) # each row contains the SNP of individuals

(result <- ssp(bmh(genotype), genotype)) 

hsphase documentation built on May 2, 2019, 3:44 p.m.