wakefield_pp

a vector of univariate pvalues from a GWAS

a vector of minor allele frequencies taken from some reference population.

a scalar or vector for total sample size of GWAS

a scalar representing the proportion of cases (n.cases/N)

a scalar representing the prior probability (DEFAULT \(1 \times 10^{-4}\))

pi_i

a scalar representing our prior expectation of \(\beta\) (DEFAULT 0.2).
The method assumes a normal prior on the population log relative risk centred at 0 and the DEFAULT
value sets the variance of this distribution to 0.04, equivalent to a 95\
is in the range of 0.66-1.5 at any causal variant.

sd.prior

if FALSE (DEFAULT), p is a p value. If TRUE, p is a log(p) value. Use this if your dataset holds p values too small to be accurately stored without using logs

log.p

This function is verbatim of its namesake in cupcake package (github.com/ollyburren/cupcake/)

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".

Guillermo Reales

RapidoPGS

A Fast and Light Package to Compute Polygenic Risk Scores

Chris Wallace

Olly Burren

wakefield_pp function

compute posterior probabilities using Wakefield's approximate Bayes Factors
<code>wakefield_pp</code> computes posterior probabilities for a given SNP to be causal for a given SNP under the assumption of a single causal variant. — wakefield_pp

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

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.

Description

Usage

Arguments

Value