A Fast and Light Package to Compute Polygenic Risk Scores.
RápidoPGS
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:
News
- In version 2.3.0, we updated the
rapidopgs_multi()
andgwascat.download()
functions. Forrapidopgs_multi()
, we udpated it to accomodate changes on susieR. Now sample size is required for all files, and thepi_i
argument has been deprecated. We also opened the possibility to apply RápidoPGS to non-European ancestries. Forgwascat.download()
, we updated the method, which wasn't working anymore to extract data from GWAS catalog. It now works interactively, providing the users advice on which file to choose. We also updated the hg38 LD blocks file, as it was updated in its original repository. - In version 2.2.0, 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).
- 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 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 2.1.0.9007 we fixed a bug caused by changes in behavior of
runsusie()
inrapidopgs_multi()
that used to supply an extra zero element which is not supplied anymore. - 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 inrunsusie()
internal function that was preventingrapidopgs_multi()
to run properly. - 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 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 (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).