ApplyPolygenicScore: Utilities for the Application of a Polygenic Score to a VCF
Simple and transparent parsing of genotype/dosage data
from an input Variant Call Format (VCF) file, matching of genotype
coordinates to the component Single Nucleotide Polymorphisms (SNPs)
of an existing polygenic score (PGS), and application of SNP weights
to dosages for the calculation of a polygenic score for each individual
in accordance with the additive weighted sum of dosages model. Methods
are designed in reference to best practices described by
Collister, Liu, and Clifton (2022) <doi:10.3389/fgene.2022.818574>.
| Version: |
4.0.2 |
| Depends: |
R (≥ 4.2.0) |
| Imports: |
vcfR, pROC, data.table, BoutrosLab.plotting.general, lattice |
| Suggests: |
knitr, rmarkdown, scales, testthat (≥ 3.0.0) |
| Published: |
2026-02-26 |
| DOI: |
10.32614/CRAN.package.ApplyPolygenicScore |
| Author: |
Paul Boutros [cre],
Nicole Zeltser 
[aut],
Rachel Dang [ctb],
Raag Agrawal [ctb] |
| Maintainer: |
Paul Boutros <PBoutros at sbpdiscovery.org> |
| License: |
GPL-2 |
| NeedsCompilation: |
no |
| Materials: |
README, NEWS |
| CRAN checks: |
ApplyPolygenicScore results |
Documentation:
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