Package: ApplyPolygenicScore
Type: Package
Title: Utilities for the Application of a Polygenic Score to a VCF
Version: 4.0.2
Authors@R: c(
    person('Paul', 'Boutros', role = 'cre', email = 'PBoutros@sbpdiscovery.org'),
    person('Nicole', 'Zeltser', role = 'aut', comment = c(ORCID = '0000-0001-7246-2771')),
    person('Rachel', 'Dang', role = 'ctb'),
    person('Raag', 'Agrawal', role = 'ctb'))
Description: 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>.
Depends: R (>= 4.2.0)
Imports: vcfR, pROC, data.table, BoutrosLab.plotting.general, lattice
Suggests: knitr, rmarkdown, scales, testthat (>= 3.0.0)
Config/testthat/edition: 3
License: GPL-2
Encoding: UTF-8
RoxygenNote: 7.3.2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2026-07-05 02:43:51 UTC; root
Author: Paul Boutros [cre], Nicole Zeltser [aut] (ORCID:
        <https://orcid.org/0000-0001-7246-2771>), Rachel Dang [ctb],
        Raag Agrawal [ctb]
Maintainer: Paul Boutros <PBoutros@sbpdiscovery.org>
Config/pak/sysreqs: libicu-dev libjpeg-dev libpng-dev
Repository: https://pboutros.r-universe.dev
Date/Publication: 2026-02-26 19:10:02 UTC
RemoteUrl: https://github.com/cran/ApplyPolygenicScore
RemoteRef: HEAD
RemoteSha: 9adad0eef19189e15dfe1c07a8dd8a272a0ef539