snp_thr_correct {bigsnpr}

Thresholding and correction

Description

P-value thresholding and correction of summary statistics for winner's curse.

Usage

snp_thr_correct(beta, beta_se, lpS, thr_lpS)

Arguments

beta

Vector of effect sizes.

beta_se

Vector of standard errors for beta. Either beta_se or lpS must be provided.

lpS

Vector of -log10(p-value) associated with beta. Either beta_se or lpS must be provided.

thr_lpS

Threshold on lpS (-log10(p-value) at which variants are excluded if they not significant enough.

Value

beta after p-value thresholding and shrinkage.

References

Zhong, H., & Prentice, R. L. (2008). Bias-reduced estimators and confidence intervals for odds ratios in genome-wide association studies. Biostatistics, 9(4), 621-634.

Examples

beta <- rnorm(1000)
beta_se <- runif(1000, min = 0.3, max = 0.5)
new_beta <- snp_thr_correct(beta, beta_se = beta_se, thr_lpS = 1)
plot(beta / beta_se, new_beta / beta_se, pch = 20); abline(0, 1, col = "red")
plot(beta, new_beta, pch = 20); abline(0, 1, col = "red")

# Can provide -log10(p-values) instead of standard errors
lpval <- -log10(pchisq((beta / beta_se)^2, df = 1, lower.tail = FALSE))
new_beta2 <- snp_thr_correct(beta, lpS = lpval, thr_lpS = 1)
all.equal(new_beta2, new_beta)