getPvalBH: Corrected p values using Benjamini & Hochberg approach

In isglobal-brge/CNVassoc: Association analysis of CNVs and imputed SNPs incorporating uncertainty

Description

This functions corrects the association p-values using the Benjamini & Hochberg approachby for multiple testing.

Usage

getPvalBH(x)

Arguments

x	a list containing p values

Details

This function calls 'p.adjust' to compute 'BH' correction

Value

A data frame with the blocks and corrected p-values

See Also

p.adjust

Examples

data(SNPTEST)
nSNP <- nrow(cases)
probs <- lapply(1:nSNP, function(i) {
    snpi.cases <- matrix(as.double(cases[i, 6:ncol(cases)]), ncol = 3, 
                        byrow = TRUE)
    snpi.controls <- matrix(as.double(controls[i, 6:ncol(controls)]), ncol = 3, 
                        byrow = TRUE)
    return(rbind(snpi.cases, snpi.controls))
})
casecon <- rep(1:0, c(500, 500))
pvals <- multiCNVassoc(probs, formula = "casecon~CNV", model = "add",
                        num.copies = 0:2, cnv.tol = 0.001)
pvalsBH <- getPvalBH(pvals)
head(pvalsBH)

isglobal-brge/CNVassoc documentation built on May 30, 2019, 9:48 p.m.