founderLine: Identifies the matriline or patriline to which each...

In matthewwolak/nadiv: (Non)Additive Genetic Relatedness Matrices

Identifies the matriline or patriline to which each individual in a pedigree belongs

Description

For every individual in a pedigree, the function identifies either the one female or male ancestor that is a founder (defined here as an individual identity in the pedigree for which both dam and sire information are missing).

Usage

founderLine(pedigree, sex)

Arguments

pedigree	A pedigree where the columns are ordered ID, Dam, Sire, Sex
sex	Character indicating the column name in pedigree identifying either the dam (for matriline) or sire (for patriline) identities

Details

Missing parents (e.g., base population) should be denoted by either 'NA', '0', or '*'.

Individuals with a missing parent for the column identified by the 'sex' argument are assigned themselves as their founder line. Thus, the definition of the founder population from a given pedigree is simply all individuals with missing parents (and in this case just a single missing parent classifies an individual as a founder).

Value

A vector of length equal to the number of rows in the pedigree

Author(s)

[e-mail]

Examples

 founderLine(FG90, sex = "dam")  # matriline from this example pedigree

 #Create random pedigree, tracking the matrilines
 ## Then compare with founderLine() output
 K <- 8  # No. individuals per generation (KEEP and even number)
 gen <- 10 # No. of generations
 datArr <- array(NA, dim = c(K, 5, gen))
 dimnames(datArr) <- list(NULL, 
c("id", "dam", "sire", "sex", "matriline"), NULL)
 # initialize the data array
 datArr[, "id", ] <- seq(K*gen)
 datArr[, "sex", ] <- c(1, 2)
 femRow <- which(datArr[, "sex", 1] == 2) # assume this is same each generation
 # (Why K should always be an even number)
 datArr[femRow, "matriline", 1] <- femRow
 # males have overlapping generations, BUT females DO NOT
 for(g in 2:gen){
   datArr[, "sire", g] <- sample(c(datArr[femRow-1, "id", 1:(g-1)]),
size = K, replace = TRUE)
   gdams <- sample(femRow, size = K, replace = TRUE)
   datArr[, c("dam", "matriline"), g] <- datArr[gdams, c("id", "matriline"), g-1]
 }
 ped <- data.frame(apply(datArr, MARGIN = 2, FUN = function(x){x}))
 nrow(ped)
 #Now run founderLine() and compare
 ped$line <- founderLine(ped, sex = "dam")
 stopifnot(identical(ped$matriline, ped$line),
	sum(ped$matriline-ped$line, na.rm = TRUE) == 0,
	range(ped$matriline-ped$line, na.rm = TRUE) == 0)

matthewwolak/nadiv documentation built on July 7, 2023, 1:24 p.m.