RápidoPGS

A rápido and lightweight method to compute Polygenic Risk Scores.

Last update: 2021-06-09

Current version: 2.1.0.9003

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 preprint:

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

News

• In version 2.1.0 we added a functionality to rapidopgs_multi(), which now allows users to use their own LD matrices instead of computing them on the go from a reference panel. For European datasets, we recommend downloading UK Biobank LD matrices kindly provided by Privé et al., which can be accessed here.

Installation

RápidoPGS (1.0.2) is now available on CRAN. You can install it by typing the code below.

install.packages("RapidoPGS")

Since we are constantly improving the package, and CRAN version is currently outdated, we recommend to install the development version instead.

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.

bigsnpr

Current bigsnpr development version (v1.6.7 as of 2021-03-08) is available from GitHub:

remotes::install_github('privefl/bigsnpr')

coloc

We used a development branch of coloc package, which can be installed by typing:

remotes::install_github('chr1swallace/coloc', ref="susie")

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).

At the moment, vignettes cover rapidopgs_single() only, but we’ll try to add a tutorial for rapidopgs_multi() soon.