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PONG2: KIR Genotype Imputation and Model Training from SNP Array Data

A scalable and accurate tool for Killer-cell Immunoglobulin-like Receptor (KIR) genotype imputation directly from SNP array data using supervised machine learning models trained across five continental ancestry groups. Uses attribute bagging and an ensemble classifier method with haplotype inference for SNPs and KIR types. Models are built from global populations in the 1000 Genomes Project and validated across diverse biobank cohorts. Methods are based on Zheng et al. (2014) <doi:10.1016/j.ajhg.2013.12.015> and Sadeeq et al. (2026) <https://github.com/NormanLabUCD/PONG2>.

Version: 1.0.1
Depends: R (≥ 4.0.0)
Imports: parallel, graphics, stats, utils, tools
LinkingTo: Rcpp, RcppParallel
Suggests: HIBAG, knitr, rmarkdown, pkgdown, testthat
Published: 2026-06-24
DOI: 10.32614/CRAN.package.PONG2 (may not be active yet)
Author: Suraju A. Sadeeq [aut, cre], Laura A. Leaton [aut], Katherine M. Kichula [aut], Paul J. Norman [aut], Xiuwen Zheng [ctb, cph] (Original HIBAG C++ code adapted in src/PONG.cpp and src/LibKIR.cpp)
Maintainer: Suraju A. Sadeeq <suraju.sadeeq at cuanschutz.edu>
BugReports: https://github.com/NormanLabUCD/PONG2/issues
License: GPL-3
URL: https://normanlabucd.github.io/PONG2/, https://github.com/NormanLabUCD/PONG2
NeedsCompilation: yes
SystemRequirements: PLINK2 (>= 2.0), minimac4 (>= 4.1.6, optional)
Materials: README
CRAN checks: PONG2 results

Documentation:

Reference manual: PONG2.html , PONG2.pdf
Vignettes: PONG2 R API: Direct R Usage with Example Data (source, R code)
PONG2 Basics: Installation, Quick Start, and Core Usage (source, R code)
PONG2 Imputation Workflow (source, R code)
PONG2 Training: Building Custom KIR Prediction Models (source, R code)

Downloads:

Package source: PONG2_1.0.1.tar.gz
Windows binaries: r-devel: not available, r-release: PONG2_1.0.1.zip, r-oldrel: not available
macOS binaries: r-release (arm64): PONG2_1.0.1.tgz, r-oldrel (arm64): PONG2_1.0.1.tgz, r-release (x86_64): PONG2_1.0.1.tgz, r-oldrel (x86_64): PONG2_1.0.1.tgz

Linking:

Please use the canonical form https://CRAN.R-project.org/package=PONG2 to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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