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A demonstration breeding population

Source: R/data.R
demoBreeding.Rd

A small, five-generation breeding population supplied so that every function in the package can be tried on data that behaves like a real programme.

Usage

data(demoBreeding)

Format

A BreedingExperiment with 900 markers and 120 genotyped individuals, and a pedigree of 180. colData holds:

generation

Generation number, 3 to 5 for genotyped individuals.

sex

"F" or "M".

yield

A moderately heritable trait (\(h^2 \approx 0.35\)), recorded on females only.

stature

A more heritable trait (\(h^2 \approx 0.60\)), recorded on everyone.

trueBV_yield, trueBV_stature

The simulated true breeding values.

Source

Simulated by data-raw/make_demo.R in the package sources.

Details

The data are simulated, not observed. They are built to have the awkward features that real breeding data has and that tidy textbook examples lack:

  • Only part of the population is genotyped. The two earliest generations were born before genotyping began, so 60 of the 180 individuals in the pedigree have no markers. This is the situation Hmatrix() exists for.

  • Unequal family sizes, because a few sires are used heavily.

  • A trait recorded on one sex only. yield is missing for males, as a milk trait would be.

  • Missing genotype calls, at about one per cent, as any chip has.

  • Markers on ten chromosomes with irregular spacing, so subsetting by genomic region is meaningful.

Because the data are simulated, the true breeding values are known and are kept in colData, which makes the object useful for checking that a prediction method recovers what it should.

See also

simulateBreeding() to generate your own, Hmatrix() for the analysis this data set is shaped for.

Examples

data(demoBreeding)
demoBreeding
#> class: BreedingExperiment
#> markers: 900  individuals genotyped: 120 
#> assays(1): genotype
#> phenotypes(6): generation sex yield stature trueBV_yield trueBV_stature
#> sequences(10): chr1 chr2 chr3 chr4 chr5 chr6
#> pedigree: 180 individuals (120 genotyped, 60 not; 30 founders)

# 60 of the 180 individuals in the pedigree were never genotyped
nrow(pedigree(demoBreeding)) - ncol(demoBreeding)
#> [1] 60

# the single-step matrix covers all of them
H <- Hmatrix(demoBreeding)
dim(H)
#> [1] 180 180