hscovar: Calculation of Covariance Between Markers for Half-Sib Families
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>.
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