prsPlot: Plot PRS performance (R-squared)

In andreyshabalin/simPRS: Fast Simulation of Polygenic Risk Scores

Description

Plot PRS performance (R-squared) with a confidence band.

Usage

prsPlot(pv, r, confInt)

Arguments

pv, r	Vectors of p-value thresholds and asymptotic correlations with phenotype, as produced by prsInf.
confInt	Upper and lower boundaries of the confidence band, as returned by rConfInt.

Details

The plot uses reverse log10 scale for the p-value threshold axis (horizontal).

Value

The function returns nothing.

Author(s)

Andrey A Shabalin [e-mail]

Examples

NTotalSNPs = 10000
NSignalSnps = 100
heritability = 0.2
signalDistr = "Same"
Ntrain = 10000
Ntest = 3000

signal = genSignal(
            NSignalSnps = NSignalSnps,
            NTotalSNPs = NTotalSNPs,
            heritability = heritability,
            signalDistr = signalDistr)
            
gwas = gwasFast(signal = signal, N = Ntrain)

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

rci = rConfInt(r = prs$r, N = Ntest)

prsPlot(pv = prs$pv, r = prs$r, rci)

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