{pangoRo} - An R package for working with COVID-19 PANGO lineages


I’ve always found working with the COVID-19 PANGO lineages a bit confusing, so I made an R package to make it easier…

Want to know the expanded names of BL.1? Want to collapse B.1.1.529. to a shorter form? This is possible in the {pangoRo} package. You can read more about it and install from GitHub https://github.com/al-obrien/pangoRo. This package was inspired by a similar package available for Python called pango_aliasor.

A few notes on functionality:

  • Caches alias table per R session to avoid unnecessary calls back to PANGO source
  • Helper functions to access various PANGO tables
  • Expand or collapse vectors of COVID-19 lineages
  • Sort lineages
  • List lineage parents and children
  • Search a lineage name to see if related to another, either as a parent or child lineage

Quick example below …


# Test vector
cov_lin <- c( 'BL.2', 'B.1.1.529.', 'XD.1')

# Create object to access alias table
my_pangoro <- pangoRo()

# Expand
expand_pangoro(my_pangoro, cov_lin)

# Collapse
collapse_pangoro(my_pangoro, cov_lin)

# Sort
sort_pangoro(my_pangoro, exp_lin)

# Search
search_pangoro(my_pangoro, 'BA.1', 'BL.1')

Welcome @al-obrien and thanks for sharing this!

@BryanTegomoh may find this of interest

Thanks @al-obrien. This is of great value!! I did reach out to Cornelius Roemer, the developer of the python package Pango Aliasor, about considering an R friendly version of pango_aliasor several weeks ago, and I think he was working on it. I didn’t have time to build one. This would be extremely valuable to the genomic epidemiology community. Thanks @neale. This is great. Some of these nested pango aliases are tough to keep straight. The big challenge would be keeping track of the evolving pango designation. I have tested this out on a dataset, and it did pretty well. It missed one or two pango_lineages, but looks like a lag on the pango side. I will let Cornelius and the team know about this development. Thanks again @al-obrien for developing this. Will certainly reach out with suggestions to improve the package. Great work!!

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Thanks @BryanTegomoh for doing some tests; I’m glad you like it and it has worked outside the ivory tower. Happy to hear any thoughts on making the package better for the community.