Crandore Hub

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>.

Versions across snapshots

VersionRepositoryFileSize
0.4.2 rolling source/ R- hscovar_0.4.2.tar.gz 178.0 KiB
0.4.2 rolling linux/jammy R-4.5 hscovar_0.4.2.tar.gz 301.8 KiB
0.4.2 rolling linux/noble R-4.5 hscovar_0.4.2.tar.gz 301.8 KiB
0.4.2 latest source/ R- hscovar_0.4.2.tar.gz 178.0 KiB
0.4.2 latest linux/jammy R-4.5 hscovar_0.4.2.tar.gz 301.8 KiB
0.4.2 latest linux/noble R-4.5 hscovar_0.4.2.tar.gz 301.8 KiB
0.4.2 2026-04-26 source/ R- hscovar_0.4.2.tar.gz 178.0 KiB
0.4.2 2026-04-23 source/ R- hscovar_0.4.2.tar.gz 178.0 KiB
0.4.2 2026-04-09 windows/windows R-4.5 hscovar_0.4.2.zip 305.2 KiB
0.4.2 2025-04-20 source/ R- hscovar_0.4.2.tar.gz 178.0 KiB

Dependencies (latest)

Imports