S1_haplo: Phase S1 parent and reconstruct progeny in terms of parental...
| S1_haplo | R Documentation |
Phase S1 parent and reconstruct progeny in terms of parental haplotypes
Description
Phase S1 parent and reconstruct progeny in terms of parental haplotypes
Usage
S1_haplo(geno, error, n.core = 1)
Arguments
geno |
ordered genotype matrix (markers x indiv) for one chromosome |
error |
average genotype error to use for the HMM |
n.core |
number of cores (default is 1) |
Details
It is assumed that only segregating markers are present. Progeny reconstruction occurs using an HMM with a uniform transition probability matrix, based on an average recombination frequency r, and a uniform model for the genotype error.
Value
List containing
- parent
two column matrix (rows = markers) with the haplotypes for the parent
- progeny
matrix with progeny reconstructed based on dosage of the second parental haplotype
