R Observatory: Metrics for RapidoPGS version 2.3.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

RapidoPGS

2.3.2Package record

A Fast and Light Package to Compute Polygenic Risk Scores

0packages depend

2.3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Guillermo RealesCRAN page ↗

Quickly computes polygenic scores from GWAS summary statistics of either case-control or quantitative traits without parameter tuning. Reales,G., Vigorito, E., Kelemen,M., Wallace,C. (2021) doi:10.1101/2020.07.24.220392 "RápidoPGS: A rapid polygenic score calculator for summary GWAS data without a test dataset".

Changes in 2.3.2

RapidoPGS 2.3.2

2026-03-30

Fixed issues with GenomeInfoDb that caused RapidoPGS to be archived on CRAN.

From NEWS.md in the release

Install

R (CRAN)Ubuntu (r2u)

install.packages("RapidoPGS", 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-rapidopgs

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 4.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK5 OK2026-04-03

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.3.2

READMEYes · 560 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 2.3.2Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 14
Examples that run: 50%2 run in a plain check · 2 never run
Exported functions with examples: 80%
Documented parameters: 98%
Return-value docs: 80%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

2.3K

CRAN downloads in the past year

Rank #9,397 · ~6/day · ~190/mo

Releases R versions

Daily download trend is not available in this view yet.

43130 days

1K90 days

2.3K1 year

Compare downloads with other packages →

Also on135 r2u

How downloads are counted

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing RapidoPGS adds 72 packages (41 with compiled code, 61 MB of source tarballs). Heaviest: BH 14 MB, ggplot2 6.0 MB, data.table 5.7 MB. 2 more not on CRAN are not measured.

Depends (5)

R >= 4.3data.table RCurl curl magrittr

Imports (6)

dplyr GenomicRanges IRanges (>= 2.34.1)bigsnpr coloc bigreadr (>= 0.2.5)

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown GenomeInfoDb

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Guillermo Reales

Author, Maintainer since 1.0.2 (2020)

Chris Wallace

Author

Olly Burren

Contributor

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-04-03
2.3.2Latest
record
2026-04-03 · current release · diff ↗
archivedRemoved from CRAN
2025-11-07
issues were not corrected despite reminders
R
R 4.5.0 released · 2025-04-11
2.3.1
record
2025-02-19 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.3.0
record
2023-10-13 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.2.0
record
2022-06-15 · diff ↗
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2021-06-17
2.1.0
record
2021-06-17 · diff ↗ ·
removed 1 export
computePGS

added 4 exports
create_1000G, rapidopgs_multi, rapidopgs_single, sd.prior.est
archivedRemoved from CRAN
2021-05-24
requires archived package 'bigsnpr'
R
R 4.1.0 released · 2021-05-18
1.0.2
record
2020-08-07

Show 1 earlier eventHide 1 earlier event

R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-08-07
Total releases: 6 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.3
Bundled data: 3.5 MB / 4 files
Download size: 3.6 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("RapidoPGS")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for RapidoPGS version 2.3.2 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →