Package: RapidoPGS 2.3.2

RapidoPGS: A Fast and Light Package to Compute Polygenic Risk Scores

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".

Authors:Guillermo Reales [aut, cre], Chris Wallace [aut], Olly Burren [ctb]

RapidoPGS_2.3.2.tar.gz
RapidoPGS_2.3.2.zip(r-4.7-any)RapidoPGS_2.3.2.zip(r-4.6-any)RapidoPGS_2.3.2.zip(r-4.5-any)
RapidoPGS_2.3.2.tgz(r-4.6-any)RapidoPGS_2.3.2.tgz(r-4.5-any)
RapidoPGS_2.3.2.tar.gz(r-4.7-any)RapidoPGS_2.3.2.tar.gz(r-4.6-any)
RapidoPGS_2.3.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RapidoPGS/json (API)

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

Bug tracker:https://github.com/grealesm/rapidopgs/issues

Datasets:

On CRAN:

Conda:

6.07 score 14 stars 14 scripts 443 downloads 5 exports 80 dependencies

Last updated from:bb8946b9e0. Checks:7 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develERROR204
source / vignettesOK405
linux-releaseERROR205
macos-releaseERROR260
macos-oldrelERROR151
windows-develERROR181
windows-releaseERROR136
windows-oldrelERROR161
wasm-releaseOK131

Exports:create_1000Ggwascat.downloadrapidopgs_multirapidopgs_singlesd.prior.est

Dependencies:BHbigassertrbigparallelrbigreadrbigsnprbigsparserbigstatsrbigutilsrBiocGenericsbitbitopsclicodetoolscoloccowplotcpp11crayoncurldata.tableDEoptimRdigestdoParalleldoRNGdplyrfarverffflockforeachgenericsGenomicRangesggplot2gluegridExtragtableIRangesirlbaisobanditeratorslabelinglatticelifecyclemagrittrMatrixmatrixStatsmixsqpnaborparallellypillarpkgconfigplyrpsR6RColorBrewerRcppRcppArmadilloRcppEigenRCurlreshapeRhpcBLASctlrlangrmiorngtoolsrobustbaseroptimRSpectrarunonceS4VectorsS7scalesSeqinfosusieRtibbletidyselecttriebeardurltoolsutf8vctrsviridisviridisLitewithr

Computing a PGS using RápidoPGS-multi
Introduction | Installation of RápidoPGS | Setup | Preparing reference panel | Preparing LD matrices (UK Biobank case) | Loading data | Computing a PGS using RápidoPGS-multi and LD matrices | Computing a PGS using RápidoPGS-multi and 1000 Genomes Phase III panel | Conclusion
Rendered fromComputing_RapidoPGSmulti.Rmdusingknitr::rmarkdown

Last update: 2026-03-30
Started: 2021-04-14

Computing a PGS using RápidoPGS-single and GWAS catalog
Introduction | Installation of RápidoPGS | Setup | Downloading data from GWAS catalog | Applying quality control to the dataset | Computing PGS using RápidoPGS-single | Applying different thresholds | Conclusion
Rendered fromComputing_RapidoPGSsingle.Rmdusingknitr::rmarkdown

Last update: 2026-03-30
Started: 2021-04-14