Jacquard (version 1.0.2)

CalculateMom: Calculate Moment Estimators for Relatedness Parameters

Description

Function CalculateMom computes moment estimators for a set of relatedness parameters (kinship, inbreeding, least one IBD out of three and T4) using the genotype data and the allele frequencies.

Usage

CalculateMom(Xgen, mafvec, ind.sub = 1:nrow(Xgen), verbose = TRUE)

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)

Arguments

Xgen

Genotype data coded in (0,1,2) format

mafvec

A vector of minor allele frequencies

ind.sub

Index for subsetting individuals

verbose

Print output on the progress of the algorithm if verbose=TRUE.

Author

Jan Graffelman ([e-mail])

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").

See Also

BoxplotTheta

Examples

data(SimulatedPedigree)
Xgen <- as.matrix(SimulatedPedigree[,6:ncol(SimulatedPedigree)])
mafvec <- mafvector(Xgen)
Theta.mom <- CalculateMom(Xgen[1:10,],mafvec)