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RápidoPGS

CRAN status

A rápido and lightweight method to compute Polygenic Risk Scores.

Last update: 2023-10-12

Current version: 2.3.0

This package allows to quickly (rápido is Spanish for “fast”) compute polygenic scores (PGS) from case-control or quantitative trait GWAS summary statistic datasets, without the need of an external validation dataset.

Background

You can find a description of the ideas behind RápidoPGS, as well as technical details in our Bioinformatics paper:

Reales G, Vigorito E, Kelemen M, & Wallace C (2021) RápidoPGS: A rapid polygenic score calculator for summary GWAS data without validation dataset. Bioinformatics, 37(23), 4444-50.

News

Installation

RápidoPGS (2.2.0) is now available on CRAN. You can install it by typing the code below.

install.packages("RapidoPGS")

Development version

There’s also a development version, that can be installed from GitHub.

library(remotes)
install_github('GRealesM/RapidoPGS')

A note on dependencies

RápidoPGS has some dependencies that aren’t available directly from CRAN, so must be installed a bit differently.

GenomicRanges

GenomicRanges package is a Bioconductor package. Please type:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GenomicRanges")

Documentation

Full documentation and vignettes are available on the website (click on the cat if you’re at the GitHub repo).

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.