grs.plot: Diagnostic plot for genetic risk score calculation from...

In gtx: Genetics ToolboX

Description

Each SNP is plotted by coefficient in the risk score (x axis) versus estimated effect size for trait of interest in the testing dataset (y axis). A solid red line shows the effect size estimate for the risk score on the trait of interest in the testing dataset.

Usage

grs.plot(w, b, s, text = NULL, textpos = NULL, textcex = 0.5,
         alpha = 0.05)

Arguments

w	coefficients for the risk score.
b	aligned beta coefficients in the testing dataset.
s	standard errors for b.
text	optional labels for SNPs
textpos	position for labels for SNPs, as pos argument to text().
textcex	size for lables for SNPs, as cex argument to text().
alpha	determines size of confidence limits plotted.

Author(s)

Toby Johnson [e-mail]

Examples

data(t2dex)
library(survival)
mycoxph <- coxph(Surv(FollowupDays,FollowupT2D) ~ Overweight,
                 data = t2dex$data) # fit null model
data(t2d.scores)
assoc1 <- grs.onesnp.apply(t2d.scores, mycoxph) # single SNP association
## risk score fit from single SNPs
grs.plot(t2d.scores$coef, assoc1$beta, assoc1$se, t2d.scores$name)
title(xlab = "risk score weight", ylab = "estimated effect size")

Example output

Loading required package: survival

gtx documentation built on May 2, 2019, 5:08 a.m.