makehap {hsrecombi} | R Documentation |
Make list of imputed sire haplotypes
Description
List of sire haplotypes is set up in the format required for
hsrecombi. Sire haplotypes are imputed from progeny genotypes using R
package hsphase
.
Usage
makehap(sireID, daughterSire, genotype.chr, nmin = 30, exclude = NULL)
Arguments
sireID |
vector (LEN N) of IDs of all sires |
daughterSire |
vector (LEN n) of sire ID for each progeny |
genotype.chr |
matrix (DIM n x p) of progeny genotypes (0, 1, 2) on a single chromosome with p SNPs; 9 indicates missing genotype |
nmin |
scalar, minimum required number of progeny for proper imputation, default 30 |
exclude |
vector (LEN < p) of SNP indices to be excluded from analysis |
Value
list (LEN 2) of lists. For each sire:
famID
list (LEN N) of vectors (LEN n.progeny) of progeny indices relating to lines in genotype matrix
sireHap
list (LEN N) of matrices (DIM 2 x p) of sire haplotypes (0, 1) on investigated chromosome
References
Ferdosi, M., Kinghorn, B., van der Werf, J., Lee, S. & Gondro, C. (2014) hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups BMC Bioinformatics 15:172. https://CRAN.R-project.org/package=hsphase
Examples
data(targetregion)
hap <- makehap(unique(daughterSire), daughterSire, genotype.chr)