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✨
DESCRIPTION |NEWS
card.svg |card.png
ApplyPolygenicScore/json (API)

# Install 'ApplyPolygenicScore' in R:

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

On CRAN:

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 333 downloads 19 exports 48 dependencies

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

Target	Result	Time
linux-devel-x86_64	OK	283
source / vignettes	OK	258
linux-release-x86_64	OK	261
macos-release-arm64	OK	147
macos-oldrel-arm64	OK	156
windows-devel	OK	217
windows-release	OK	198
windows-oldrel	OK	215
wasm-release	OK	146

Exports:analyze.pgs.binary.predictiveness apply.polygenic.score assess.pgs.vcf.allele.match combine.pgs.bed combine.vcf.with.pgs convert.allele.frequency.to.dosage convert.alleles.to.pgs.dosage convert.pgs.to.bed create.pgs.boxplot create.pgs.density.plot create.pgs.rank.plot create.pgs.with.continuous.phenotype.plot flip.DNA.allele format.chromosome.notation get.pgs.percentiles import.pgs.weight.file import.vcf parse.pgs.input.header run.pgs.regression

Dependencies:ape BoutrosLab.plotting.general class cli cluster data.table deldir digest dplyr e1071 generics glue gridExtra gtable hexbin interp jpeg lattice latticeExtra lifecycle magrittr MASS Matrix memuse mgcv nlme permute pillar pinfsc50 pkgconfig png pROC proxy R6 RColorBrewer Rcpp RcppEigen rlang stringi stringr tibble tidyselect utf8 vcfR vctrs vegan viridisLite withr

User Guide

Rendered fromUserGuide.Rmdusingknitr::rmarkdown

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

Help page	Topics
Analyze PGS Predictiveness for Binary Phenotypes	analyze.pgs.binary.predictiveness
Apply polygenic score to VCF data	apply.polygenic.score
Assess PGS allele match to VCF allele	assess.pgs.vcf.allele.match
Check PGS weight file columns	check.pgs.weight.columns
Combine PGS BED files	combine.pgs.bed
Combine VCF with PGS	combine.vcf.with.pgs
Convert allele frequency to mean dosage	convert.allele.frequency.to.dosage
Convert alleles to dosage	convert.alleles.to.pgs.dosage
Convert PGS data to BED format	convert.pgs.to.bed
Plot PGS Boxplots	create.pgs.boxplot
Plot PGS Density	create.pgs.density.plot
Plot PGS Rank	create.pgs.rank.plot
Plot PGS Scatterplots	create.pgs.with.continuous.phenotype.plot
Flip DNA allele	flip.DNA.allele
Format chromosome names	format.chromosome.notation
get.pgs.percentiles	get.pgs.percentiles
Import PGS weight file	import.pgs.weight.file
Import VCF file	import.vcf
Parse PGS input file header	parse.pgs.input.header
Run linear and logistic regression on a polygenic score and a set of phenotypes	run.pgs.regression
Write apply.polygenic.score output to file	write.apply.polygenic.score.output.to.file

Package: ApplyPolygenicScore 4.0.2

ApplyPolygenicScore: Utilities for the Application of a Polygenic Score to a VCF

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)