RapidoPGS v1.0.2

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A Fast and Light Package to Compute Polygenic Risk Scores

Quickly computes polygenic scores from GWAS summary statistics of either case-control or quantitative traits, without LD matrix computation or parameter tuning. Reales,G., Kelemen,M., Wallace,C. (2020) <doi:10.1101/2020.07.24.220392> "R<c3><a1>pidoPGS: A rapid polygenic score calculator for summary GWAS data without validation dataset".

Readme

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.

Functions in RapidoPGS

Name Description
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).
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Vignettes of RapidoPGS

Name
Computing_RapidoPGS.Rmd
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Details

License GPL-3
Encoding UTF-8
LazyData true
RoxygenNote 7.1.1
VignetteBuilder knitr
NeedsCompilation no
Packaged 2020-08-03 17:58:48 UTC; guille
Repository CRAN
Date/Publication 2020-08-07 14:20:02 UTC

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