wakefield_pp_quant: Compute posterior probabilities using Wakefield's approximate...

In RapidoPGS: A Fast and Light Package to Compute Polygenic Risk Scores

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

Description

wakefield_pp_quant computes posterior probabilities for a given SNP to be causal for a given SNP under the assumption of a single causal variant.

Usage

wakefield_pp_quant(beta, se, sdY, sd.prior = 0.15, pi_i = 1e-04)

Arguments

beta	a vector of effect sizes (\beta) from a quantitative trait GWAS
se	vector of standard errors of effect sizes (\beta)
sdY	a scalar of the standard deviation given vectors of variance of coefficients, MAF and sample size. Can be calculated using sdY.est
sd.prior	a scalar representing our prior expectation of \beta (DEFAULT 0.15).
pi_i	a scalar representing the prior probability (DEFAULT 1 \times 10^{-4}) 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.

Details

This function was adapted from wakefield_pp in cupcake package (github.com/ollyburren/cupcake/)

Value

a vector of posterior probabilities.

Author(s)

Guillermo Reales, Chris Wallace

RapidoPGS documentation built on Oct. 13, 2023, 5:11 p.m.