cad.scores: Genetic risk scores for coronary artery disease risk

In gtx: Genetics ToolboX

Description

Risk score parameterised using GWAS meta-analysis results published by the C4D and CARDIoGRAM consortia (C4D Consortium Nature Genetics 2011, Schunkert et al. Nature Genetics 2011). The score is for risk of prevalent coronary artery disease (CAD).

Usage

data(cad.scores)

Format

A data frame suitable for use with other functions in this package, see gtx.params.

The score is called CAD2011, and has coefficients in ln(odds) for CAD per coded allele. For details of how results from the two papers were combined, see manuscript by T. Johnson.

Source

For the publications from which these data were extracted see http://dx.doi.org/10.1038/ng.782 and http://dx.doi.org/10.1038/ng.784.

Examples

data(cad.scores)
cad.scores$MAF <- pmin(cad.scores$coded.freq, 1-cad.scores$coded.freq)
cad.scores$OR <- exp(abs(cad.scores$coef))
plot(cad.scores$MAF, cad.scores$OR,
     xlim = c(0, 0.5), ylim = c(1, max(cad.scores$OR)),
     xlab = "Minor allele frequency",
     ylab = "Odds ratio effect", las = 1)
text(cad.scores$MAF, cad.scores$OR, cad.scores$name, pos = 1, cex = 0.5)

Example output

Loading required package: survival

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