optiSel (version 2.0.9)

pedIBD: Calculates the Pedigree-based Kinship Matrix

Description

Calculates the pedigree based probability of alleles to be IBD. This pedigree based kinship matrix is also called coancestry matrix and is half the additive relationship matrix.

Usage

pedIBD(Pedig, keep.only=NULL, keep=keep.only, kinFounder=NULL)

Value

Kinship matrix.

Arguments

Pedig

Data frame containing the pedigree with Indiv (individual ID), Sire, and Dam in the first 3 columns. Missing parents are coded as NA. Both parents must either be missing or present. If this is not the case use function prePed to prepare the pedigree.

keep

If keep is provided then kinships are computed only for these animals and their ancestors.

keep.only

If keep.only is provided then kinships are computed only for these animals.

kinFounder

Kinship matrix for the founders. The row names are the ids of the founders. By default, founders are assumed to be unrelated. Founders not included in this matrix are also assumed to be unrelated.

Author

Robin Wellmann

Details

Computation of pedigree based kinship matrix f which is half the additive relationship matrix. For individuals i and j it is defined as

fij = Probability that two alleles chosen from individuals i and j are IBD.

Examples

data(PedigWithErrors)
data(Phen)
keep  <- Phen$Indiv
Pedig <- prePed(PedigWithErrors, keep=keep, thisBreed="Hinterwaelder", lastNative=1970)
pedA  <- pedIBD(Pedig, keep.only=keep)