matLD

<p>(p x p) matrix of maternal LD between pairs of p markers;
  matrix is block diagonal in case of multiple chromosomes</p>

datasets

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

Calculation of Covariance Between Markers for Half-Sib Families

Michael Doschoris

Jan Klosa

matLD function

<p>An object of class <code>matrix</code> (inherits from <code>array</code>) with 300 rows and 300 columns.</p>

matLD: testdata: maternal linkage disequilibrium

Description

Usage

Arguments

Format