get_pedigree: Generate pedigree
In jendelman/polyBreedR: Genomics-assisted breeding for polyploids (and diploids)

get_pedigree

R Documentation

Generate pedigree

Description

Generate pedigree for a set of individuals

Usage

get_pedigree(id, pedfile, delim = ",", na.string = "NA", trim = TRUE)

Arguments

`id`	Vector of names of individuals
`pedfile`	Name of pedigree file
`delim`	Delimiter for the pedigree file (default is "," for CSV)
`na.string`	String used for NA in the pedigree file (default is "NA")
`trim`	TRUE/FALSE whether to trim pedigree (see Details)

Details

Finds ancestors of individuals in a three-column pedigree file (id,mother,father). The id column can be the identifier for an individual or cross. String matches must be exact or based on the naming convention crossID-progenyID. The returned pedigree is ordered using R package pedigree so that offspring follow parents. When trim is TRUE (default), the pedigree is trimmed to remove ancestors with only one offspring (which are not needed to compute the pedigree relationship matrix).