Using py‐ard in R

Using py-ard from R Programming Language

py-ard requires Python 3.8 or higher. Install Python using your package manager or from Python Homepage.

You can create a virtual environment with:

cd <your-project-dir>
python3 -m venv venv
source venv/bin/activate 

Install reticulate R package

The R library reticulate allows calling Python packages from R.

install.packages('reticulate')

Install py-ard from R

Load reticulate library in R.

library(reticulate)

If using virtual environments, call use_virtualenv function to point to the virtual environment you created.

use_virtualenv('venv/')

Verify your Python environment

py_config()

This should show you the Python installation that reticulate is using.

Install py-ard in the Python environment

py_install('py-ard')

Use py-ard from R

Import pyard library and get the ARD python object.

pyard <- import('pyard')
ard <- pyard$init()
reduced_alleles <- ard$redux('A*01:01:01/A*01:AB', 'lgx')

Produces:

> reduced_alleles
[1] "A*01:01/A*01:01/A*01:02"

Available reduction modes are G, lg, lgx, W and exon.

Methods can be called on the ard object using the $ operator. Eg. can call expand_mac to get back a vector of expanded alleleles for a MAC code.

 > ard$expand_mac("A*03:AAAUY")
 [1] "A*03:01"   "A*03:01N"  "A*03:20"   "A*03:21N"  "A*03:26"   "A*03:37"   "A*03:45"   "A*03:78"  
 [9] "A*03:112"  "A*03:118"  "A*03:129N" "A*03:132"  "A*03:134"  "A*03:162N" "A*03:182"