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 SNPBLUP approach. The implementation relies on paternal halfsib families and biallelic markers. If maternal halfsib families are used, the roles of sire/dam are swapped. Multiple families can be considered. Wittenburg, Bonk, Doschoris, Reyer (2020) "Design of Experiments for FineMapping Quantitative Trait Loci in Livestock Populations" <doi:10.1186/s12863020008711>. Carlson, Eberle, Rieder, Yi, Kruglyak, Nickerson (2004) "Selecting a maximally informative set of singlenucleotide polymorphisms for association analyses using linkage disequilibrium" <doi:10.1086/381000>.
Package details 


Author  Dörte Wittenburg [aut, cre], Michael Doschoris [aut], Jan Klosa [ctb] 
Maintainer  Dörte Wittenburg <wittenburg@fbndummerstorf.de> 
License  GPL (>= 2) 
Version  0.4.2 
Package repository  View on CRAN 
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