CCT: An analytical p-value combination method using the Cauchy...

In weizhouUMICH/SAIGE: Efficiently controlling for case-control imbalance and sample relatedness in single-variant assoc tests (SAIGE) and controlling for sample relatedness in region-based assoc tests in large cohorts and biobanks (SAIGE-GENE)

An analytical p-value combination method using the Cauchy distribution

Description

The CCT function takes in a numeric vector of p-values, a numeric vector of non-negative weights, and return the aggregated p-value using Cauchy method.

Usage

CCT(pvals, weights = NULL)

Arguments

pvals	a numeric vector of p-values, where each of the element is between 0 to 1, to be combined.
weights	a numeric vector of non-negative weights. If NULL, the equal weights are assumed.

Value

the aggregated p-value combining p-values from the vector pvals.

References

Liu, Y., & Xie, J. (2020). Cauchy combination test: a powerful test with analytic p-value calculation under arbitrary dependency structures. Journal of the American Statistical Association 115(529), 393-402. (pub)

Examples

pvalues <- c(2e-02,4e-04,0.2,0.1,0.8)
CCT(pvals=pvalues)

weizhouUMICH/SAIGE documentation built on May 6, 2022, 12:34 a.m.