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RápidoPGS

A rápido and lightweight method to compute Polygenic Risk Scores.

Last update: 2020-08-03

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, Kelemen M, & Wallace C (2020) RápidoPGS: A rapid polygenic score calculator for summary GWAS data without validation dataset. BioRxiv.

Installation

library(remotes)
install_github('GRealesM/RapidoPGS')

Documentation

Full documentation and vignettes are available on the website.

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Version

Install

install.packages('RapidoPGS')

Monthly Downloads

275

Version

1.0.2

License

GPL-3

Maintainer

Guillermo Reales

Last Published

August 7th, 2020

Functions in RapidoPGS (1.0.2)

logsum

Helper function to sum logs without loss of precision
michailidou

Subset of Michailidou BRCA GWAS sumstat dataset.
wakefield_pp_quant

Compute posterior probabilities using Wakefield's approximate Bayes Factors for quantitative traits
sdY.est

Estimate trait variance, internal function
wakefield_pp

compute posterior probabilities using Wakefield's approximate Bayes Factors wakefield_pp computes posterior probabilities for a given SNP to be causal for a given SNP under the assumption of a single causal variant.
gwascat.download

Retrieve GWAS summary datasets from GWAS catalog 'gwascat.download takes a PMID from the user and downloads the associated summary statistics datasets published in GWAS catalog
computePGS

Compute PGS from GWAS summary statistics using posteriors from Wakefield's approximate Bayes Factors
EUR_ld.blocks38

LD block architecture for European populations (hg38).
EUR_ld.blocks

LD block architecture for European populations (hg19).