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