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

In xihaoli/STAAR: STAAR Procedure for Dynamic Incorporation of Multiple Functional Annotations in Whole-Genome Sequencing Studies

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 (default = NULL).

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)

Liu, Y., et al. (2019). Acat: A fast and powerful p value combination method for rare-variant analysis in sequencing studies. The American Journal of Human Genetics, 104(3), 410-421. (pub)

Examples

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

xihaoli/STAAR documentation built on Jan. 27, 2024, 8:51 a.m.