pACAT: Cauchy Combination Test

In SAIGEgds: Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies

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))

SAIGEgds documentation built on Nov. 8, 2020, 7:46 p.m.