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>.

Getting started

Package details

AuthorDörte Wittenburg [aut, cre], Michael Doschoris [aut], Jan Klosa [ctb]
MaintainerDörte Wittenburg <wittenburg@fbn-dummerstorf.de>
LicenseGPL (>= 2)
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:

Try the hscovar package in your browser

Any scripts or data that you put into this service are public.

hscovar documentation built on April 13, 2021, 9:06 a.m.