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

In rmsharp/nprcmanager: Genetic Tools for Colony Management

Get Genetic Value Genotype data structure for reportGV function.

Description

Extracts genotype data if available otherwise NULL is returned.

Usage

getGVGenotype(ped)

Arguments

ped	the pedigree information in datatable format

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.

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)

rmsharp/nprcmanager documentation built on Feb. 2, 2025, 12:45 a.m.