pACAT {SAIGEgds} | R Documentation

## Cauchy Combination Test

### Description

P-value calculation from Cauchy combination test.

### Usage

    pACAT(p, w=NULL)
    pACAT2(p, maf, wbeta=c(1,25))

### Arguments

`p` | a numeric vector for p-values
`w` | weight for each p-value
`maf` | minor allele frequency for each p-value
`wbeta` | weights for per-variant effect, using beta distribution `dbeta()` according to variant's MAF

### Value

Return a single number for the combined p-value.

### References

Liu Y., Cheng S., Li Z., Morrison A.C., Boerwinkle E., Lin X.; ACAT: A Fast and Powerful p Value Combination Method for Rare-Variant Analysis in Sequencing Studies. Am J Hum Genetics 104, 410-421 (2019).

### See Also

`seqFitNullGLMM_SPA`, `seqAssocGLMM_SPA`

### Examples

    p1 <- 10^-4
    p2 <- 10^-5
    p3 <- 10^-(3:20)
    sapply(p3, function(p) pACAT(c(p1, p2, p)))

    pACAT2(c(10^-4, 10^-6), c(0.01, 0.005))

[Package SAIGEgds version 1.4.0 Index]