multiCNVassoc: Association between several CNVs and disease

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

Description

This function repeatedly calls CNVassoc function

Usage

multiCNVassoc(x, formula, num.copies = 0:2, cnv.tol = 0.01, ...)

Arguments

x	a list of calling probabilities matrix for each CNV
formula	see 'formula' argument of CNVassoc function.
num.copies	See argument of cnv function.
cnv.tol	See argument of cnv function.
...	other arguments passed through 'CNVassoc' function.

Details

See vignette for more examples example

Value

A list of p-values for each CNV

References

Gonzalez JR, Subirana I, Escaramis G, Peraza S, Caceres A, Estivill X and Armengol L. Accounting for uncertainty when assessing association between copy number and disease: a latent class model. BMC Bioinformatics, 2009;10:172.

See Also

CNVassoc

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.