Package: ApplyPolygenicScore
Type: Package
Title: Utilities for the Application of a Polygenic Score to a VCF
Version: 4.0.1
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: 2026-01-23 23:15:37 UTC; rhughwhite
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>
Repository: CRAN
Date/Publication: 2026-01-24 00:20:13 UTC
Built: R 4.5.2; ; 2026-01-26 00:52:28 UTC; windows
