README.md

In BrnCPrz/PedyR: Handles genealogical structured data

PedyR

R package to deal with pedigrees.

upcoming updates: * pedStats() - A function for more in depth description of a pedigree. * getBdate() - Estimates a birth date for animals without that record in the pedigree. * getFounder() - Calculates the effective number of founders for a pedigree.

General Functions (version 0.1.4 - Aug 8, 2016)

For now, PedyR package has the following functions:

checkPed()

Checks for the (most common) errors in pedigrees, such as duplicated ids, sire and dams with the same ids, etc...

getF()

Calculates the inbreeding coefficient [1] for each individual in the pedigree.

getGen()

Calculates the generation of each individual in the pedigree.

getOrdPed()

A function to order a pedigree using the Kahn's topological sorting algorithm [2].

effSize()

Calculates the effective population size for a given pedigree using methods discribed in [3].

Example:

id = c(1,2,3,4,5,6,7,8,9,10)
sire = c(0,0,1,1,3,5,5,5,7,7)
dam = c(0,0,2,2,2,4,4,6,6,8)
ped = as.data.frame(cbind(id,sire,dam))
checkPed(ped)
ped$F = getF(ped)
ped$Gen = getGen(ped)

Authors

• Bruno C. Perez - GitHub
• Gerson A. Oliveira Junior - GitHub

Contributing

Please feel free to submit new ideas, code corrections or pull requests to us.

License

This project is licensed under the MIT License.

References

• [1] Meuwissen THE and Luo Z, 1992. Computing inbreeding coefficients in large populations. Genet. Sel. Evol. 24, 305-313.
• [2] Kahn AB, 1962. "Topological sorting of large networks", Communications of the ACM.
• [3] Gutiérrez, JP, Cervantes I, Goyache F, (2009). "Improving the estimation of realized effective populationsizes in farm animals", J. Anim. Breed. Genet., 126, 327-332.

BrnCPrz/PedyR documentation built on May 6, 2019, 8:47 a.m.