addGenotype: Add genotype data to pedigree file

In nprcgenekeepr: Genetic Tools for Colony Management

Add genotype data to pedigree file

Description

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.

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).

Value

A pedigree object with genotype data added.

Examples

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

nprcgenekeepr documentation built on July 26, 2026, 5:06 p.m.