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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: 3.0.1
Depends: R (≥ 4.2.0)
Imports: vcfR, pROC, data.table, reshape2, BoutrosLab.plotting.general, lattice
Suggests: knitr, rmarkdown, testthat (≥ 3.0.0)
Published: 2025-03-05
DOI: 10.32614/CRAN.package.ApplyPolygenicScore
Author: Paul Boutros [cre], Nicole Zeltser ORCID iD [aut], Rachel Dang [ctb]
Maintainer: Paul Boutros <PBoutros at mednet.ucla.edu>
License: GPL-2
NeedsCompilation: no
Materials: README NEWS
CRAN checks: ApplyPolygenicScore results

Documentation:

Reference manual: ApplyPolygenicScore.pdf
Vignettes: User Guide (source, R code)

Downloads:

Package source: ApplyPolygenicScore_3.0.1.tar.gz
Windows binaries: r-devel: ApplyPolygenicScore_3.0.1.zip, r-release: ApplyPolygenicScore_3.0.1.zip, r-oldrel: ApplyPolygenicScore_3.0.1.zip
macOS binaries: r-devel (arm64): ApplyPolygenicScore_3.0.1.tgz, r-release (arm64): ApplyPolygenicScore_3.0.1.tgz, r-oldrel (arm64): ApplyPolygenicScore_3.0.1.tgz, r-devel (x86_64): ApplyPolygenicScore_3.0.1.tgz, r-release (x86_64): ApplyPolygenicScore_3.0.1.tgz, r-oldrel (x86_64): ApplyPolygenicScore_3.0.1.tgz

Linking:

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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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