CalculateTheta {Jacquard} | R Documentation |
Function CalculateTheta
calculates five identifiable relatedness parameters from a
list structure containing nine matrices of Jacquard coefficients.
CalculateTheta(J, ind.sub = 1:nrow(J[[1]]))
J |
A list structure with nine matrices of pairwise Jacquard coefficients |
ind.sub |
Index for subsetting the individuals |
CalculateTheta
produces four matrices according to the expressions in
Graffelman et al. (2024).
A list object with four fields:
T1 |
The pairwise coancestry or kinship coefficients (symmetric) |
T2 |
The pairwise inbreeding coefficients (non-symmetric) |
T3 |
The pairwise Least one IBD out of three (symmetric) |
T4 |
T4 (skew-symmetric) |
Jan Graffelman (jan.graffelman@upc.edu)
Csuros, M. (2014) Non-identifiability of identity coefficients at biallelic loci. Theoretical Population Biology 92, pp. 22-29. 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 doi:10.1101/2024.03.25.586682.
data(DeltaSimulatedPedigree)
Theta <- CalculateTheta(DeltaSimulatedPedigree)