createSimKinships: Makes a list object of kinship matrices from simulated...

In rmsharp/nprcmanager: Genetic Tools for Colony Management

Makes a list object of kinship matrices from simulated pedigrees of possible parents for animals with unknown parents

Description

createSimKinships uses makeSimPed with the ped object and the allSimParents object to create a set of kinship matrices to be used in forming the Monte Carlo estimates for the kinship values.

Usage

createSimKinships(ped, allSimParents, pop = NULL, n = 10L, verbose = FALSE)

Arguments

ped	The pedigree information in data.frame format
allSimParents	list made up of lists where the internal list has the offspring ID, id, a vector of representative sires (sires), and a vector of representative dams (dams).
pop	Character vector with animal IDs to consider as the population of interest. This allows you to provide a pedigree in ped that has more animals than you want to use in the simulation by defining pop with the subset of interest. The default is NULL.
n	integer value of the number of simulated pedigrees to generate.
verbose	logical vector of length one that indicates whether or not to print out when an animal is missing a sire or a dam.

Value

A list of n lists with each internal list containing a kinship matrix from simulated pedigrees of possible parents for animals with unknown parents.

Examples

library(nprcgenekeepr)
ped <- nprcgenekeepr::smallPed
simParent_1 <- list(id = "A",
                    sires = c("s1_1", "s1_2", "s1_3"),
                    dams = c("d1_1", "d1_2", "d1_3", "d1_4"))
simParent_2 <- list(id = "B",
                    sires = c("s2_1", "s2_2", "s2_3"),
                    dams = c("d2_1", "d2_2", "d2_3", "d2_4"))
simParent_3 <- list(id = "E",
                    sires = c("s3_1", "s3_2", "s3_3"),
                    dams = c("d3_1", "d3_2", "d3_3", "d3_4"))
allSimParents <- list(simParent_1, simParent_2, simParent_3)
pop <- LETTERS[1:7]
simKinships <- createSimKinships(ped, allSimParents, pop, n = 10)

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