pruneped: Pedigree pruning

In ggroups: Pedigree and Genetic Groups

Pedigree pruning

Description

Pruning pedigree in two different modes (strict, loose)

Usage

pruneped(ped, pheno, mode)

Arguments

ped	: data.frame with integer columns corresponding to ID, SIRE, DAM. Missing value is 0.
pheno	: Vector of phenotyped individuals
mode	: strict or loose

Details

In strict pruning, individuals without progeny and phenotype are recursively deleted from the pedigree, and then individuals without known parent and without progeny (if any) are deleted. Therefore, all uninfluential individuals are deleted. The downside is that individuals without phenotype or phenotyped progeny cannot receive any genetic merit based on the information from their phenotyped relatives. In loose pruning, the pedigree is upward extracted for phenotyped individuals to thier founders, and then the pedigree is downward extracted from the founders.

Value

Pruned pedigree data.frame

Examples

ped = data.frame(ID=1:7, SIRE=c(0,0,1,3,1,4,0), DAM=c(0,0,2,2,2,5,0))
pheno = c(1,4)
pruneped(ped, pheno, mode="strict")
pruneped(ped, pheno, mode="loose")

ggroups documentation built on March 28, 2022, 1:06 a.m.