liver.scores: Genetic risk scores for liver enzyme traits.

In gtx: Genetics ToolboX

Description

Risk scores parameterised using GWAS meta-analysis results published by Chambers et al. (Nature Genetics 2011) for serum ALT, ALP and GGT levels.

Usage

data(liver.scores)

Format

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

The scores are called ALT2011, ALP2011 and GGT2011, for serum concentrations of alanine transaminase (ALT), alkaline phosphatase (ALP) and gamma-glutamyl transferase (GGT). The first twelve columns of data were taken from Table 1 of Chambers et al. (2011). Effect sizes (coef) are on log10(concentration) scale, from inverse variance weighted meta-analyses over 17 studies, with analysed sample sizes 45596, 56415 and 61089, for ALT, ALP and GGT respectively. Two additional columns of data (beta_replication and se_replication) were taken from Supplementary Table 18 of Chambers et al. (2011), and give the effect size and SE (back calculated from the reported P-value) in an independent replication sample of size 8112.

Source

For the publication by Chambers et al. from which these data were extracted see http://dx.doi.org/10.1038/ng.970.

Examples

data(liver.scores)
with(subset(liver.scores, score == "ALP2011"), {
  plot(pmin(coded.freq, 1 - coded.freq), coef,
       xlab = "MAF", ylab = "ALP effect",
       xlim = c(0, 0.5), ylim = c(0, 10), las = 1)
  text(pmin(coded.freq, 1 - coded.freq), coef, name,
       pos = 3, cex = 0.5)})
## compare unweighted score used by Chambers et al. 2011
## with weighted score:
with(subset(liver.scores, score == "ALP2011"),
     rbind(unlist(grs.summary(rep(1, length(coef)), beta_replication,
                              se_replication, n = 8112)),
           unlist(grs.summary(coef, beta_replication,
                              se_replication, n = 8112))))

Example output

Loading required package: survival
      m    n      X2m        R2m      ahat        aSE     X2rs       R2rs
[1,] 14 8112 468.9801 0.05617369 2.5035835 0.14244639 308.9024 0.03736377
[2,] 14 8112 468.9801 0.05617369 0.9136978 0.04335698 444.1064 0.05327521
             pval       Qrs         phet
[1,] 3.787348e-69 160.07771 1.901086e-27
[2,] 1.382751e-98  24.87369 2.398158e-02

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