prsInf: Calculate Asymptotic Performance of Poligenic Risk Score

In andreyshabalin/simPRS: Fast Simulation of Polygenic Risk Scores

Description

Calculate asymptotic performance of poligenic risk score (PRS) at all possible p-value thresholds.

Usage

prsInf(gwasBt, gwasPV, signal)

Arguments

gwasBt, gwasPV	Vectors of effect size estimates and p-values for all SNPs. Can be generated with gwasFast.
signal	Vector of effect sizes for all SNPs. Usually the one used to generate the GWAS summary statistics.

Details

The function does not generate the artificial genotype and phenotype. Instead, finite sample distribution of the summary statistics is used for generation of the output.

Value

The function returns the vector of p-value thresholds (sorted vector of GWAS p-values, pv) and corresponding asymptotic correlations of the phenotype with PRS (r).

Author(s)

Andrey A Shabalin [e-mail]

Examples

signal = genSignal(
            NSignalSnps = 10,
            NTotalSNPs = 20,
            heritability = 0.1,
            signalDistr = "Same")
            
gwas = gwasFast(signal = signal, N = 85)

cbind(beta = gwas$beta, pv = gwas$pv)

prs = prsInf(
            gwasPV = gwas$pv,
            gwasBt = gwas$beta,
            signal = signal)

cbind(pv = prs$pv, r = prs$r)

andreyshabalin/simPRS documentation built on May 21, 2019, 2 p.m.