Add genotype data to pedigree file

Assumes genotype has been opened by checkGenotypeFile

Usage

addGenotype(ped, genotype)

Arguments

ped

pedigree dataframe. ped is to be provided by qcStudbook so it is not checked.

genotype

genotype dataframe. genotype is to be provided by checkGenotypeFile so it is not checked.

Value

A pedigree object with genotype data added.

Details

The two allele columns are coerced to character internally so the name-keyed allele dictionary is both built and indexed by allele label. This keeps the integer encoding consistent even when the allele columns are supplied as factors (a factor would otherwise be indexed by its integer codes).

Examples

library(nprcgenekeepr)
rhesusPedigree <- nprcgenekeepr::rhesusPedigree
rhesusGenotypes <- nprcgenekeepr::rhesusGenotypes
pedWithGenotypes <- addGenotype(
  ped = rhesusPedigree,
  genotype = rhesusGenotypes
)