gtx (version 0.0.7)

grs.filter.Qrs: Filter SNPs for inclusion in genetic risk score using heterogeneity test.

Description

Performs a stepwise downward model selection in which SNPs are iteratively removed from the risk score until the heterogeneity test is no longer significant at the specified threshold.

Usage

grs.filter.Qrs(w, b, s, p.thresh = 0.05)

Arguments

w

coefficients for the risk score

b

aligned beta coefficients in the testing dataset

s

standard errors

p.thresh

P-value threshold

Details

When there are m SNPs in the risk score, the heterogeneity test is an (m-1) d.f. LRT comparing the 1 d.f. risk score model against the unconstrained m d.f. model, as reported by the Qrs element of grs.summary. At each iteration, if the risk score model has a significant heterogeneity test (at p.thresh), the SNP is removed that gives the greatest decrease in the heterogeneity test statistic.

Examples

data(magic.scores)
  score1 <- subset(magic.scores, score == "FG2010")
  score1 <- within(score1, okay <- grs.filter.Qrs(coef, beta_TG, se_TG))
  with(score1, {grs.plot(coef, beta_TG, se_TG, locus);
    title(xlab = "FG effect", ylab = "TG effect")})
  with(score1, locus[!okay]) # loci removed
  with(subset(score1, okay), {grs.plot(coef, beta_TG, se_TG, locus);
    title(xlab = "FG effect", ylab = "TG effect")})