RápidoPGS

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

  • 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.
  • In development version 2.1.0.9005 we fixed a change in the hard-coded url to download 1000G panel from the official server to meet a change in versioning for sex chromosomes at the source.
  • In development version 2.1.0.9006 we fixed an error popping up when rapidopgs_multi() is not supplied input of data.table class, and removed a deprecated argument in runsusie() internal function that was preventing rapidopgs_multi() to run properly.
  • In development version 2.1.0.9007 we fixed a bug caused by changes in behavior of runsusie() in rapidopgs_multi() that used to supply an extra zero element which is not supplied anymore.
  • In development version 2.1.0.9008 we fixed a change in the hard-coded url to download 1000G panel from the official server to meet a change in versioning (v5a -> v5b) at the source.
  • In development version 2.1.0.9009 we fixed a bug derived from automatically supplying “nref” to SuSIE in rapidopgs_multi(), which is no longer required.
  • In version 2.2.0.9000 we updated hg38 LD blocks from liftovered Berisa & Pickrell to recomputed MacDonald et al. 2022 (https://github.com/jmacdon/LDblocks_GRCh38, https://www.biorxiv.org/content/10.1101/2022.03.04.483057v1).

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).