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:
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 inrunsusie()
internal function that was preventingrapidopgs_multi()
to run properly. - 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 2.1.0.9008 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 (2.1.0) 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).