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The main goal of developing this package is to construct an R-based front-end to connect to the Practical Haplotype Graph - a general, graph-based, computational framework for genotype inference.


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,


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")