R code to select breeders from an advanced intercross line so that they minimize inbreeding in the offspring
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#Breeder selection in advanced intercross lines

This repository contains R source code to select breeders in an advanced intercross line so that inbreeding in the offspring is minimized.

  • kinship.R defines functions to calculate and update pairwise kinship coefficients.

  • find_mates.R pairs breeders in a given generation of the advanced intercross line in such a way that they will produce the smallest average inbreeding coefficients in the offspring.

See example.R for an example of how to use these functions to select mouse breeders in generation F10 of an advanced intercross line. The pedigree data for this mouse population are found in data. This script should generate matings similar to those in F10pairs.txt.