OneMap tutorial

A tutorial on how to use OneMap and the accompanying software fullsibQTL.

These R Markdown files were written to accompany lectures in the course “Genetic Mapping”, taught at the University of Wisconsin-Madison in the spring of 2021.

• Part 1 introduces the package, and demonstrates how to form linkage groups using a dataset from an F1 apple population.

• Part 2 uses this same apple dataset to illustrate how recombination frequencies are estimated between biallelic SNPs, and subsequently ordered within linkage groups.

• Part 3 demonstrates why multiallelic markers are more informative in determining marker order and phase using a dataset from an F1 family of clownfish.

• Part 4 uses the F1 apple population and the genetic maps constructed using onemap to demonstrate the use of the companion QTL mapping software fullsibQTL.