Jacquard (version 1.0.2)

BoxplotTheta: Boxplots of Relateness parameters

Description

Function BoxplotTheta makes boxplots of relatedess parameters from a list object containing estimates of pairwise relatedness parameters.

Usage

BoxplotTheta(KS, ind.sub = 1:nrow(KS[[1]]), ...)

Value

NULL

Arguments

KS

A list object with four fields of matrices: kinship, inbreeding, T3 and T4.

ind.sub

Index for subsetting the individuals

...

Additional arguments passed on to the function boxplot.

Author

Jan Graffelman ([e-mail])

Details

For individual inbreeding coefficients, two boxplots are made, the first based on the diagonal of T2, the second on the row means of T2. The remaining boxplots (kinship, T3 and T4) are all pairwise, and exclude self-pairs.

References

Csuros, M. (2014) Non-identifiability of identity coefficients at biallelic loci. Theoretical Population Biology 92, pp. 22-29. tools:::Rd_expr_doi("10.1016/j.tpb.2013.11.001").

Graffelman, J., Weir, B.S. and Goudet, J. (2024) Estimation of Jacquard's genetic identity coefficients with bi-allelic variants by constrained least-squares. Preprint at bioRxiv tools:::Rd_expr_doi("10.1101/2024.03.25.586682").

See Also

CalculateTheta

Examples

data(DeltaSimulatedPedigree)
Theta <- CalculateTheta(DeltaSimulatedPedigree)
BoxplotTheta(Theta)