H.sire

<p>(2N x p) matrix of sire haplotypes for all chromosomes (2 lines
  per sire); unknown alleles are marked as 9</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

H.sire function

<p>An object of class <code>matrix</code> (inherits from <code>array</code>) with 10 rows and 300 columns.</p>

H.sire: testdata: sire haplotypes

Description

Usage

Arguments

Format