pedBreedComp: Calculates the Pedigree Based Breed Composition of...

In optiSel: Optimum Contribution Selection and Population Genetics

Calculates the Pedigree Based Breed Composition of Individuals

Description

Computes for every individual the genetic contribution from native founders and from other breeds according to the pedigree.

Usage

pedBreedComp(Pedig, thisBreed)

Arguments

Pedig	Data frame containing the pedigree with the first 3 columns being Indiv (individual ID), Sire, and Dam. Additional columns include column Breed with breed names. Missing parents are coded as NA. All animals have no parent or both parents missing. It is usually created with function prePed.
thisBreed	Name of the breed of interest as denoted in column Breed of the pedigree.

Details

For every individual the genetic contribution from native founders and from other breeds is computed. It is the fraction of genes that originate from the respective breed.

Value

Data frame with one row for each individual and the following columns

Indiv	IDs of the individuals
native	Native Contribution: The genetic contribution from native founders.
...	Genetic contributions from other breeds, one column for each breed. The columns are ordered, so that the most influential breeds come first.

Author(s)

Robin Wellmann

Examples

data(ExamplePed)
Pedig    <- prePed(ExamplePed, thisBreed="Hinterwaelder", lastNative=1970)
cont     <- pedBreedComp(Pedig, thisBreed="Hinterwaelder")
cont[1000:1010,2:5]

contByYear <- conttac(cont, Pedig$Born, use=Pedig$Breed=="Hinterwaelder", mincont=0.04, long=FALSE)
round(contByYear,2)

barplot(contByYear,ylim=c(0,1), col=1:10, ylab="genetic contribution",
        legend=TRUE, args.legend=list(x="bottomleft",cex=0.6))

optiSel documentation built on Sept. 11, 2024, 7:19 p.m.