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.
You can find a description of the ideas behind RápidoPGS, as well as technical details in our Bioinformatics paper:
rapidopgs_multi()
and gwascat.download()
functions. For rapidopgs_multi()
, we udpated it to accomodate changes on susieR. Now sample size is required for all files, and the pi_i
argument has been deprecated. We also opened the possibility to apply RápidoPGS to non-European ancestries. For gwascat.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.rapidopgs_multi()
, which is no longer required.runsusie()
in rapidopgs_multi()
that used to supply an extra zero element which is not supplied anymore.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.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.RápidoPGS (2.2.0) is now available on CRAN. You can install it by typing the code below.
install.packages("RapidoPGS")
There’s also a development version, that can be installed from GitHub.
library(remotes)
install_github('GRealesM/RapidoPGS')
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")