genMatrix: Derive genetic matrices

In QTLRel: Tools for Mapping of Quantitative Traits of Genetically Related Individuals and Calculating Identity Coefficients from Pedigrees

Derive genetic matrices

Description

Derive genetic matrices from Jacquard condensed identity coefficients or genotypic data.

Usage

genMatrix(x)

Arguments

x	An object of cic or ibs, or genotypic data in a matrix or a data frame with each row representing an individual and each column a marker locus and entry being "AA", "AB", "BB" (or 1, 2, 3) without missing genotypes.

Value

AA	Additive genetic matrix.
DD	Dominance genetic matrix.
AD,HH,MH	Other three genetic matrices (see Abney et. al. 2000).
ib	Inbreeding coefficients.

References

Abney, M., M. S. McPeek, and C. Ober (2000). Estimation of variance components of quantitative traits in inbred populations. Am. J. Hum. Genet. 141, 629-650.

See Also

cic

Examples

data(miscEx)

ids<- sample(pedF8$id[300:500],20)

## Not run: 
# get condensed identity coefficients
oo<- cic(pedF8, ids=ids, df=0)
ksp<- kinship(pedF8, ids=ids) # kinship coefficients only
# extract genetic matrices
gm<- genMatrix(oo)
sum((gm$AA-2*ksp)>1e-7) # same results

## End(Not run)

QTLRel documentation built on Aug. 9, 2023, 1:07 a.m.