pbgeno

pbgeno is an R package to streamline plant breeding data analysis and visualization. It provides functions to easily generate publication-quality tables and figures for genotype datasets.

Installation

You can install the latest version of pbgeno from GitHub:

#install.packages("devtools")
devtools::install_github("Allan-gitrepos/pbgeno")

Usage

pbgeno contains functions for common plant breeding workflows:

library(pbgeno)

# Jaccard distance matrix
dists <- ggtree_jaccard(Jaccard_example)

# Polymorphism information content
results <- pic_calc(PIC_example)

# Convert structure foramt to tassel format data
tassel_data <- str2tassel(Structure_example, metadata)

Example data

pbgeno contains some example genotype and phenotype datasets:

• Jaccard_example: SSR markers data for calculating jaccard distances
• PIC_example: SSR marker data for calculating PIC_values
• Structure_example: SSR marker data example in structure format
• metadata: Meta data for the tassel data.

Key functions

• ggtree_jaccard - Generate Jaccard distance matrix
• pic_calc - Calculate PIC value for each marker
• str2tassel - Converts Structure format data to tassel hapmap format

Getting help

If you encounter any issues or bugs with pbgeno, please file an issue on the GitHub repository. Ideas for package improvements and contributions are also welcome!