Haplo2Geno

<p>[MATRIX] haplotype matrix (2 lines per individual)</p>

inpMat

<p>Haplotypes are converted into into genotypes without checking
 for missing values.</p>

The theoretical covariance between pairs of markers is calculated
from either paternal haplotypes and maternal linkage disequilibrium (LD) or
vise versa. A genetic map is required. Grouping of markers is based on the
correlation matrix and a representative marker is suggested for each group.
Employing the correlation matrix, optimal sample size can be derived for
association studies based on a SNP-BLUP approach.
The implementation relies on paternal half-sib families and biallelic
markers. If maternal half-sib families are used, the roles of sire/dam are
swapped. Multiple families can be considered.
Wittenburg, Bonk, Doschoris, Reyer (2020) "Design of Experiments for
Fine-Mapping Quantitative Trait Loci in Livestock Populations"
<doi:10.1186/s12863-020-00871-1>.
Carlson, Eberle, Rieder, Yi, Kruglyak, Nickerson (2004) "Selecting a
maximally informative set of single-nucleotide polymorphisms for association
analyses using linkage disequilibrium" <doi:10.1086/381000>.

D<c3><b6>rte Wittenburg

hscovar

Haplo2Geno: Conversion of haplotypes into genotypes

Description

Usage

Arguments

Value

Examples