optiSel (version 0.9.1)

pedBreedComp: 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 where the first 3 columns correspond to: 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. If this is not the case use prePed.

thisBreed

Name of this breed as denoted in column (5) of the pedigree.

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.

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.

Examples

# NOT RUN {
data(ExamplePed)
Pedig    <- prePed(ExamplePed, thisBreed="Hinterwaelder", lastNative=1970)
cont     <- pedBreedComp(Pedig, thisBreed="Hinterwaelder")
Pedig$MC <- 1-cont$native
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))
# }