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