Package: hscovar 0.4.2

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>.

Authors:Dörte Wittenburg [aut, cre], Michael Doschoris [aut], Jan Klosa [ctb]

hscovar_0.4.2.tar.gz
hscovar_0.4.2.zip(r-4.5)hscovar_0.4.2.zip(r-4.4)hscovar_0.4.2.zip(r-4.3)
hscovar_0.4.2.tgz(r-4.4-any)hscovar_0.4.2.tgz(r-4.3-any)
hscovar_0.4.2.tar.gz(r-4.5-noble)hscovar_0.4.2.tar.gz(r-4.4-noble)
hscovar_0.4.2.tgz(r-4.4-emscripten)hscovar_0.4.2.tgz(r-4.3-emscripten)
hscovar.pdf |hscovar.html✨
hscovar/json (API)
NEWS

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

14 exports 0.00 score 11 dependencies 2 scripts 169 downloads

Last updated 3 years agofrom:4d08292cdd. Checks:OK: 7. Indexed: yes.

Exports:AR1calcvarCovarMatrixCovMatExpectMatHaplo2GenoLDdamLDsirepwr.normtestpwr.snpblupsearch.best.n.bisectionsimpleMstartvaluetagSNP

Dependencies:codetoolsdata.tableforeachiteratorsjsonlitelatticeMatrixpwrrlistXMLyaml