nprcgenekeepr (version 1.0.8)

getGVGenotype: Get Genetic Value Genotype data structure for reportGV function.

Description

Extracts genotype data if available otherwise NULL is returned.

Usage

getGVGenotype(ped)

Value

A data.frame with the columns id, first, and second extracted from a pedigree object (a data.frame) containing genotypic data. If the pedigree object does not contain genotypic data the NULL is returned.

Arguments

ped

the pedigree information in datatable format

Examples

## We usually defined `n` to be >= 5000
library(nprcgenekeepr)
ped <- nprcgenekeepr::lacy1989Ped
allelesNew <- geneDrop(ped$id, ped$sire, ped$dam, ped$gen,
  genotype = NULL, n = 50, updateProgress = NULL
)
genotype <- data.frame(
  id = ped$id,
  first_allele = c(
    NA, NA, "A001_B001", "A001_B002",
    NA, "A001_B002", "A001_B001"
  ),
  second_allele = c(
    NA, NA, "A010_B001", "A001_B001",
    NA, NA, NA
  ),
  stringsAsFactors = FALSE
)
pedWithGenotype <- addGenotype(ped, genotype)
pedGenotype <- getGVGenotype(pedWithGenotype)
allelesNewGen <- geneDrop(ped$id, ped$sire, ped$dam, ped$gen,
  genotype = pedGenotype,
  n = 5, updateProgress = NULL
)