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

In optiSel: Optimum Contribution Selection and Population Genetics

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))

Example output

Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 
                   native  Fleckvieh unknown Vorderwaelder
276000802918558 0.7968750 0.17187500   0.000       0.03125
276000802918459 0.6562500 0.21875000   0.000       0.12500
276000802884019 0.8925781 0.10742188   0.000       0.00000
276000802918062 0.4960938 0.12890625   0.250       0.12500
276000802918674 0.7011719 0.11132812   0.000       0.18750
276000802925588 0.6230469 0.12695312   0.000       0.25000
276000802925021 0.5683594 0.08789062   0.125       0.21875
276000802908590 0.8593750 0.14062500   0.000       0.00000
276000802898268 0.6269531 0.12304688   0.000       0.25000
276000802918887 0.7011719 0.17382812   0.000       0.12500
276000802908489 0.7578125 0.17968750   0.000       0.06250
              1948 1949 1950 1951 1952 1953 1954 1955 1956 1957 1958 1959 1960
native        0.83    1    1    1    1    1 0.91    1 0.92 0.86 0.83  0.8 0.84
Fleckvieh     0.17    0    0    0    0    0 0.09    0 0.08 0.14 0.17  0.2 0.16
Vorderwaelder 0.00    0    0    0    0    0 0.00    0 0.00 0.00 0.00  0.0 0.00
other         0.00    0    0    0    0    0 0.00    0 0.00 0.00 0.00  0.0 0.00
unknown       0.00    0    0    0    0    0 0.00    0 0.00 0.00 0.00  0.0 0.00
              1961 1962 1963 1964 1965 1966 1967 1968 1969 1970 1971 1972 1973
native        0.74 0.81 0.82 0.75 0.83 0.89 0.83 0.85 0.89 0.87 0.71 0.80 0.72
Fleckvieh     0.26 0.19 0.18 0.23 0.17 0.11 0.17 0.14 0.11 0.13 0.14 0.16 0.14
Vorderwaelder 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.09 0.03 0.10
other         0.00 0.00 0.00 0.02 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.00
unknown       0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.00 0.04
              1974 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986
native        0.81 0.68 0.77 0.68 0.69 0.65 0.63 0.64 0.68 0.65 0.66 0.59 0.64
Fleckvieh     0.11 0.16 0.12 0.14 0.12 0.11 0.11 0.10 0.11 0.11 0.10 0.10 0.10
Vorderwaelder 0.06 0.05 0.08 0.14 0.14 0.10 0.15 0.15 0.12 0.15 0.15 0.11 0.12
other         0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.02 0.00 0.00
unknown       0.02 0.10 0.03 0.04 0.05 0.13 0.11 0.12 0.09 0.09 0.07 0.20 0.14
              1987 1988 1989 1990 1991 1992 1993 1994 1995
native        0.64 0.62 0.59 0.56 0.57 0.65 0.60 0.65 0.58
Fleckvieh     0.13 0.10 0.12 0.10 0.13 0.12 0.10 0.13 0.09
Vorderwaelder 0.11 0.12 0.13 0.08 0.13 0.12 0.11 0.12 0.10
other         0.00 0.00 0.03 0.00 0.03 0.00 0.00 0.00 0.00
unknown       0.12 0.16 0.14 0.26 0.15 0.12 0.19 0.10 0.23

optiSel documentation built on March 13, 2020, 3:09 a.m.