CalculateTheta: Calculate Relatedness Paramenters from Jacquard Coefficients...

In Jacquard: Estimation of Jacquard's Genetic Identity Coefficients

Calculate Relatedness Paramenters from Jacquard Coefficients tA Capitalized Title (ideally limited to 65 characters)

Description

Function CalculateTheta calculates five identifiable relatedness parameters from a list structure containing nine matrices of Jacquard coefficients.

Usage

CalculateTheta(J, ind.sub = 1:nrow(J[[1]]))

Arguments

J	A list structure with nine matrices of pairwise Jacquard coefficients
ind.sub	Index for subsetting the individuals

Details

CalculateTheta produces four matrices according to the expressions in Graffelman et al. (2024).

Value

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)

Author(s)

Jan Graffelman ([e-mail])

References

Csuros, M. (2014) Non-identifiability of identity coefficients at biallelic loci. Theoretical Population Biology 92, pp. 22-29. \Sexpr[results=rd]{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 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1101/2024.03.25.586682")}.

See Also

Jacquard.cls

Examples

data(DeltaSimulatedPedigree)
Theta <- CalculateTheta(DeltaSimulatedPedigree)

Jacquard documentation built on Sept. 17, 2024, 5:09 p.m.