README.Rmd

---
title: "polyBreedR"
author: Jeffrey Endelman
output: github_document
---

This R package was designed to facilitate the use of genome-wide markers for breeding autotetraploid (4x) species, but it also functionality for diploids. The software has been developed and tested using data from the University of Wisconsin-Madison [potato breeding program](http://potatobreeding.cals.wisc.edu).

To install and load the package:
```R
install.packages("devtools")
library(devtools)
install_github("jendelman/polyBreedR", build_vignettes=FALSE)
library(polyBreedR)
```

### Vignettes

[Vignette 1](https://jendelman.github.io/polyBreedR/polyBreedR_Vignette1.html) covers the making of tetraploid genotype calls and their utility for pedigree curation. The pedigree functionality is based on [Endelman et al. (2017)](https://doi.org/10.1007/s12230-016-9556-y). Financial support has come from USDA NIFA Hatch Projects 1002731 and 1013047, administered through the Wisconsin Agricultural Experiment Station at UW-Madison. 

[Vignette 2](https://jendelman.github.io/polyBreedR/polyBreedR_Vignette2.html) covers the analysis of marker data for dihaploids, including checking ploidy and parentage. Financial support has come from USDA NIFA Awards 2014-67013-22434 (AFRI) and 2019-51181-30021 (SCRI).

For a complete specification of the package functions, consult the [reference manual.](https://jendelman.github.io/polyBreedR/polyBreedR_Manual.pdf)