R/checkCNV.R

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

checkCNV <- function(obj, alpha = 0.05) {
        out <- TRUE
        meanRatio <- attr(obj, "meanRatio")
        if (is.null(meanRatio)) 
            stop("CNV must contain intensity data") else {
            mins <- by(meanRatio, obj, min)
            maxs <- by(meanRatio, obj, max)
            out <- cor(mins, maxs, method = "spearman") == 
                1
        }
        pvalue <- attr(obj, "mixture")$P
        if (!is.null(pvalue)) 
            out <- !is.nan(pvalue) && pvalue >= 
                alpha && out
        return(out)
}