hscovar

Description

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>.

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Running examples in ‘hscovar-Ex.R’ failed
The error most likely occurred in:

> ### Name: tagSNP
> ### Title: tagSNP
> ### Aliases: tagSNP
> 
> ### ** Examples
> 
>   ### 1: INPUT DATA
>   data(testdata)
>   ### 2: COVARIANCE/CORRELATION MATRIX
>   c
...[truncated]...
of the job will be affected
0 SNPs have non-zero variance -> output matrix has reduced dimensions.
Error in `rownames<-`(`*tmp*`, value = 1:p) : 
  attempt to set 'rownames' on an object with no dimensions
Calls: CovMat -> rownames<-
Execution halted

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