ApplyPolygenicScore

4.0.2

Utilities for the Application of a Polygenic Score to a VCF

0packages depend

3.2Kdownloads / year

95.3%test coverage

13/13checks pass

Overview

About

Maintained by Paul BoutrosFirst published 2025-03-054 releasesCRAN page ↗

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.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)

install.packages("ApplyPolygenicScore", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-applypolygenicscore

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-ApplyPolygenicScore

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

Slowest check: 11.5 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 1.69

95.3%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-12
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-10
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMEYes · 1,225 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.2K

CRAN downloads in the past year

Rank #13,380 · ~9/day · ~270/mo

Releases R versions

Daily download trend is not available in this view yet.

24130 days

80990 days

3.2K1 year

Compare downloads with other packages →

Also on204 r2u

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2.0

Imports (5)

vcfR pROC data.table BoutrosLab.plotting.generallattice

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown scales testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 11,603 (75%)Other 1,589 (10%)Rd 1,355 (9%)Vignettes 837 (5%)

Code characteristics

Cyclomatic complexity: 4.5 median / 47 max
Test cases: 132 / 1.69 per code line

Test coverage

Line coverage

95%

Expression

94.5%

Tests / Examples

95.3% / 69% ex

Functions

46 19 exported

Complexity

8.4 avg / 47 max

Call network

46 nodes / 53 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

46 functions

Function	Cyclo	Coverage
get.non.risk.multiallelic.site.row	10	69%
validate.allele.input	5	85%
analyze.pgs.binary.predictiveness exp	47	85%
write.apply.polygenic.score.output.to.file	4	87%
validate.vcf.input	11	88%
create.pgs.density.plot exp	15	95%

People & History

People (4)

Maintainer (1)

Paul Boutros

Maintainer

Authors (1)

Nicole Zeltser

Author

Contributors (2)

Raag Agrawal

Contributor · added in 4.0.0

Rachel Dang

Contributor

Package Timeline

4 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
4.0.2Latest
2026-02-26 · current release · diff ↗
4.0.1
2026-01-24 · diff ↗
4.0.0
2025-08-21 · diff ↗
R
R 4.5.0 released · 2025-04-11
3.0.1
2025-03-05
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-03-05
Total releases: 4 / 1 yrs
License: GPL-2 OSI
Minimum R: ≥ 4.2.0
Download size: 4.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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