The goal of {quincunx} is to provide programmatic access to the
Polygenic Score (PGS) Catalog, an open
resource for polygenic
scores and associated
metadata describing their development and respective assessment.
Browse the online documentation at maialab.org/quincunx to get started.
Install {quincunx} from CRAN:
# Install from CRAN
install.packages("quincunx")You can instead install the development version of {quincunx} by
setting Ramiro Magno’s universe
repository:
options(repos = c(ramiromagno = 'https://ramiromagno.r-universe.dev',
CRAN = 'https://cloud.r-project.org'))
install.packages('quincunx'){quincunx} was published in Bioinformatics in 2021:
https://doi.org/10.1093/bioinformatics/btab522.
To generate a citation for this publication from within R:
citation('quincunx')
#>
#> To cite quincunx in publications use:
#>
#> Ramiro Magno, Isabel Duarte, Ana-Teresa Maia, quincunx: an R package
#> to query, download and wrangle PGS Catalog data, Bioinformatics,
#> btab522, 16 July 2021, Pages 1-3,
#> https://doi.org/10.1093/bioinformatics/btab522
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {quincunx: an R package to query, download and wrangle PGS Catalog data},
#> author = {Ramiro Magno and Isabel Duarte and Ana-Teresa Maia},
#> journal = {Bioinformatics},
#> year = {2021},
#> pages = {1--3},
#> url = {https://doi.org/10.1093/bioinformatics/btab522},
#> }Also, please do not forget to cite the authors behind the original studies and the papers associated with the PGS Catalog project:
- Lambert, S.A., Gil, L., Jupp, S. et al. The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation. Nat Genet 53, 420–425 (2021). doi: 10.1038/s41588-021-00783-5
- Wand, H., Lambert, S.A., Tamburro, C. et al. Improving reporting standards for polygenic scores in risk prediction studies. Nature 591, 211–219 (2021). doi: 10.1038/s41586-021-03243-6
Please note that if you use the data provided by the PGS Catalog either
directly or via {quincunx} you agree to abide to the EMBL-EBI Terms
of Use.
Please note that the {quincunx} project is released with a
Contributor Code of
Conduct. By
contributing to this project, you agree to abide by its terms.
This work would have not been possible without the precious feedback from the PGS Catalog team, particularly Samuel Lambert and Laurent Gil.
The package name {quincunx} is another name for Galton
Board, that so nicely
exemplifies the Central Limit
Theorem, which in
turn is a key concept of genetics, namely, Fisher’s infinitesimal
model… which leads us to
Polygenic Scores, the key concept of the PGS Catalog.
The bird in the hex sticker is a Porphyrio porphyrio, an emblematic species native to the Ria Formosa Natural Park, which is a wildlife reserve surrounding the University of Algarve, where the authors are affiliated.