AmatrixPolyCross: Construction of pedigree-based relationship matrix with...

In prmunoz/AGHmatrix: Relationship Matrices for Diploid and Autopolyploid Species

Construction of pedigree-based relationship matrix with parental guessing possibility

Description

Creates an additive relationship matrix A based on a non-deterministic pedigree with 4+ columns where each column represents a possible parent. This function was built with the following designs in mind. 1) A mating design where you have equally possible parents. For example, a generation of insects derived from the mating of three insects in a cage. All the insects in this generation will have the same expected relatedness with all the possible parents (1/3). If there are only two parents in the cage, the function assumes no-inbreeding and the pedigree is deterministic (the individual is offspring of the cross between the two parents). Another example, a population of 10 open-pollinated plants where you harvest the seeds without tracking the mother. 2) When fixedParent is TRUE: a mating design where you know one parent and might know the other possible parents. For example, a polycross design where you have seeds harvested from a mother plant and possible polen donors.

Usage

AmatrixPolyCross(data = NULL, fixedParent = FALSE)

Arguments

data	pedigree data name. Unknown value should be equal 0. See example for construction.
fixedParent	if false, assumes that all the parents are equally possible parents. If true, assumes that the first parental is known and the others are equally possible parents. Default = FALSE.

Value

Matrix with the relationship between the individuals.

Author(s)

Rodrigo R Amadeu, [e-mail]

Examples

#the following pedigree has the id of the individual followed by possible parents
#if 0 is unknown
#the possible parents are filled from left to right
#in the pedigree data frame examples:
#id 1,2,3,4 have unknown parents and are assumed unrelated
#id 5 has three possible parents (1,2,3)
#id 6 has three possible parents (2,3,4)
#id 7 has two parents (deterministic case here, the parents are 3 and 4)
#id 8 has four possible parents (5,6,7,1)

pedigree = data.frame(id=1:8,
                      parent1 = c(0,0,0,0,1,2,3,5),
                      parent2 = c(0,0,0,0,2,3,4,6),
                      parent3 = c(0,0,0,0,3,4,0,7),
                      parent4 = c(0,0,0,0,0,0,0,1),
                      parent5 = 0)

print(pedigree)

AmatrixPolyCross(pedigree)

#when polyCross is set to be true:
#id 5 is offspring of parent 1 in a deterministic way and two other possible parents (2,3)
#id 6 is offspring of parent 2 in a deterministic way and two other possible parents (3,4)
#id 7 has two parents (deterministic case here, the parents are 3 and 4); as before
#id 8 is offspring of parent 5 in a deterministic way and has three other possible parents (6,7,1)

AmatrixPolyCross(pedigree,fixedParent=TRUE)

prmunoz/AGHmatrix documentation built on Oct. 3, 2023, 5:43 p.m.