ACATO: omnibus aggregated Cauchy association test

In nbelon/sumSTAAR: Fast Region-Based Association Tests on Summary Statistics

Description

This test combines P values via aggregated Cauchy association test (Liu, Y. et al., 2019)

Usage

ACATO(p)

Arguments

p	a vector of P values to combine

Details

ACATO is an omnibus aggregated Cauchy association test recently proposed by Liu, Y. et al. (2019). This function can be used to combine P values obtained by different gene-based tests for the same gene (see Examples below).

Value

a single P value which is a combination of the P values given in input

References

Liu Y. et al. (2019) ACAT: a fast and powerful p value combination method for rare-variant analysis in sequencing studies. Am. J. Hum. Genet. 104, 410-421.

Examples

cor.path <- system.file("testfiles/", package = "sumFREGAT")
score.file <- system.file("testfiles/CFH.full.vcf.gz", package = "sumFREGAT")

p.bt <- BT(score.file, genes = "CFH", cor.path = cor.path)$pvalue
p.skat <- SKAT(score.file, genes = "CFH", cor.path = cor.path)$pvalue
p.pca <- PCA(score.file, genes = "CFH", cor.path = cor.path, n = 85)$pvalue

p.combined <- ACATO(c(p.bt, p.skat, p.pca))

nbelon/sumSTAAR documentation built on Dec. 22, 2021, 12:04 a.m.