RápidoPGS

CRAN status

A rápido and lightweight method to compute Polygenic Risk Scores.

Last update: 2022-06-15

Current version: 2.2.0.9000

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 (2.1.0) 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).