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>.

Version: 0.4.2
Depends: R (≥ 3.5.0)
Imports: parallel, Matrix, foreach, rlist, pwr
Published: 2021-04-13
DOI: 10.32614/CRAN.package.hscovar
Author: Dörte Wittenburg [aut, cre], Michael Doschoris [aut], Jan Klosa [ctb]
Maintainer: Dörte Wittenburg <wittenburg at fbn-dummerstorf.de>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
Materials: NEWS
CRAN checks: hscovar results


Reference manual: hscovar.pdf


Package source: hscovar_0.4.2.tar.gz
Windows binaries: r-devel: hscovar_0.4.2.zip, r-release: hscovar_0.4.2.zip, r-oldrel: hscovar_0.4.2.zip
macOS binaries: r-release (arm64): hscovar_0.4.2.tgz, r-oldrel (arm64): hscovar_0.4.2.tgz, r-release (x86_64): hscovar_0.4.2.tgz, r-oldrel (x86_64): hscovar_0.4.2.tgz
Old sources: hscovar archive


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