makePed: A function to add founders and sort pedigrees

In Victor-Oribamise/Sibs: An R Toolkit for Computation of Relatedness Measures using Large Pedigrees

Description

Raw pedigrees are typically not sorted chronologically and may be missing founders. Using the supplied pedigree, this function adds missing founders and then sorts the pedigree to ensure parents always come before offspring.

Usage

makePed(pedigree)

Arguments

pedigree

A dataframe where the first three columns correspond to ID, Sire, and Dam. Unknown parents should be given a value of zero. This function will help to add missing founders with sire and dam labeled as zero. It then sorts the pedigree to ensure that parents come before their offspring.

Value

When this function is needed, the user can load it as Ped1 = makePed(pedigree), the dataframe Ped1 will contain a new sorted and renumbered pedigree with the parents ordered before their offspring

ID	sorted animals in the pedigree
Sire	Sorted sires in the pedigree
Dam	Sorted dams in the pedigree

Note

For issues or problems with this function, please contact Victor Oribamise at [e-mail].

Author(s)

Victor Oribamise and Ernest Osanyinlokun

References

Gutierrez J.P., Goyache F. (2005): A note on ENDOG: a computer program for analysing pedigree information. Journal of Animal Breeding and Genetics, 122, 172-176.

Examples

pedigree = data.frame(ID = c(1,2,3,4,5,6,7,8), Sire = c(0,0,1,1,3,3,5,5), Dam = c(0,0,0,2,4,4,6,6))
Ped1 = makePed(pedigree)

Victor-Oribamise/Sibs documentation built on Dec. 18, 2021, 6:16 p.m.