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 (2019) "Design of Experiments for Fine-Mapping Quantitative Trait Loci in Livestock Populations" <doi:10.1101/2019.12.17.879106>. 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: 0.2.1
Depends: R (≥ 3.5.0)
Imports: parallel, Matrix, foreach, rlist, pwr
Published: 2020-04-15
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

Downloads:

Reference manual: hscovar.pdf
Package source: hscovar_0.2.1.tar.gz
Windows binaries: r-devel: hscovar_0.2.1.zip, r-release: hscovar_0.2.1.zip, r-oldrel: hscovar_0.2.1.zip
macOS binaries: r-release: hscovar_0.2.1.tgz, r-oldrel: hscovar_0.2.1.tgz
Old sources: hscovar archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=hscovar to link to this page.