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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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