Package: ApplyPolygenicScore 4.0.2

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>.

Authors:Paul Boutros [cre], Nicole Zeltser [aut], Rachel Dang [ctb], Raag Agrawal [ctb]

ApplyPolygenicScore_4.0.2.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
ApplyPolygenicScore/json (API)
NEWS

# Install 'ApplyPolygenicScore' in R:
install.packages('ApplyPolygenicScore', repos = c('https://pboutros.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.18 score 2 scripts 240 downloads 19 exports 48 dependencies

Last updated from:9adad0eef1. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK264
source / vignettesOK224
linux-release-x86_64OK269
macos-release-arm64OK261
macos-oldrel-arm64OK217
windows-develOK220
windows-releaseOK234
windows-oldrelOK227
wasm-releaseOK117

Exports:analyze.pgs.binary.predictivenessapply.polygenic.scoreassess.pgs.vcf.allele.matchcombine.pgs.bedcombine.vcf.with.pgsconvert.allele.frequency.to.dosageconvert.alleles.to.pgs.dosageconvert.pgs.to.bedcreate.pgs.boxplotcreate.pgs.density.plotcreate.pgs.rank.plotcreate.pgs.with.continuous.phenotype.plotflip.DNA.alleleformat.chromosome.notationget.pgs.percentilesimport.pgs.weight.fileimport.vcfparse.pgs.input.headerrun.pgs.regression

Dependencies:apeBoutrosLab.plotting.generalclasscliclusterdata.tabledeldirdigestdplyre1071genericsgluegridExtragtablehexbininterpjpeglatticelatticeExtralifecyclemagrittrMASSMatrixmemusemgcvnlmepermutepillarpinfsc50pkgconfigpngpROCproxyR6RColorBrewerRcppRcppEigenrlangstringistringrtibbletidyselectutf8vcfRvctrsveganviridisLitewithr

User Guide

Rendered fromUserGuide.Rmdusingknitr::rmarkdownon May 27 2026.

Last update: 2025-08-20
Started: 2025-03-05

Readme and manuals

Help Manual

Help pageTopics
Analyze PGS Predictiveness for Binary Phenotypesanalyze.pgs.binary.predictiveness
Apply polygenic score to VCF dataapply.polygenic.score
Assess PGS allele match to VCF alleleassess.pgs.vcf.allele.match
Check PGS weight file columnscheck.pgs.weight.columns
Combine PGS BED filescombine.pgs.bed
Combine VCF with PGScombine.vcf.with.pgs
Convert allele frequency to mean dosageconvert.allele.frequency.to.dosage
Convert alleles to dosageconvert.alleles.to.pgs.dosage
Convert PGS data to BED formatconvert.pgs.to.bed
Plot PGS Boxplotscreate.pgs.boxplot
Plot PGS Densitycreate.pgs.density.plot
Plot PGS Rankcreate.pgs.rank.plot
Plot PGS Scatterplotscreate.pgs.with.continuous.phenotype.plot
Flip DNA alleleflip.DNA.allele
Format chromosome namesformat.chromosome.notation
get.pgs.percentilesget.pgs.percentiles
Import PGS weight fileimport.pgs.weight.file
Import VCF fileimport.vcf
Parse PGS input file headerparse.pgs.input.header
Run linear and logistic regression on a polygenic score and a set of phenotypesrun.pgs.regression
Write apply.polygenic.score output to filewrite.apply.polygenic.score.output.to.file