zsc: Calculate Z-scores from P-values and estimated effects

In dotgen: Gene-Set Analysis via Decorrelation by Orthogonal Transformation

Calculate Z-scores from P-values and estimated effects

Description

zsc() recovers Z-scores from P-values and corresponding effect directions (or beta coefficients) reported by a genetic association analysis.

Usage

zsc(P, BETA)

Arguments

P	vector of P-values.
BETA	vector of effect directions or beta coefficients.

Details

For any genetic variant, its two-sided P-value (p) and the sign of estimated effect (\beta) is used to recover the Z-score (z), that is, z = sign(\beta) \Phi^{-1}(p/2).

Value

A vector of Z-scores.

See Also

dot()

Examples

## result of per-variant analysis (P-values and estimated effects)
res <- readRDS(system.file("extdata", 'rs208294_res.rds', package="dotgen"))

## recover Z-score statistics
stt <- with(res, zsc(P, BETA))

## checking
stopifnot(all.equal(pnorm(abs(stt), lower.tail = FALSE) * 2, res$P))

dotgen documentation built on Oct. 27, 2024, 5:07 p.m.