Objective
rPHG
is a system to interact with and retrieve information from a Practical Haplotype Graph (PHG) - a general, graph-based, computational framework for genotype inference. This is accomplished by leveraging the Breeding and PHG APIs.
Citation
To cite rPHG
, please use the following citation:
Bradbury et al. (2022). The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation. Bioinformatics, 38(15), 3698–3702, https://doi.org/10.1093/bioinformatics/btac410
Installation
If you do not have experience working with and setting up rJava
with your R installation, it is recommended that you read the long-form documentation. This walkthrough can be found here. If you are already fairly comfortable working with Java JDK and rJava
, you can follow the following commands.
Package source code can be installed directly from this BitBucket repository using the devtools
package:
if (!require("devtools")) install.packages("devtools")
devtools::install_github(repo = "maize-genetics/rPHG")