R/getQualityScore.cnv.R

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

getQualityScore.cnv <- function(x, type = "class", 
        iter = 10000, threshold = 0.1, ...) {
        obj <- x
        if (is.null(attr(obj, "means"))) {
            ff <- function(threshold) {
                res <- apply(attr(obj, "probabilities"), 
                    1, function(x) {
                    index <- which.max(x)
                    max1 <- x[index]
                    max2 <- max(x[-index])
                    (max2/max1) > threshold
                    })
                mean(res)
            }
            out <- ff(threshold)
            attr(out, "type") <- 0
            attr(out, "threshold") <- threshold
        } else {
            mu <- attr(obj, "means")
            sds <- attr(obj, "sds")
            w <- attr(obj, "pi")
            batches <- attr(x, "batches")
            if (is.null(batches)) 
                out <- getQualityScore(mu, sds, 
                    w, type, iter = iter, threshold = threshold) else {
                out <- list()
                bb <- sort(unique(batches))
                for (i in bb) out[[i]] <- getQualityScore(mu[i, 
                    ], sds[i, ], w[i, ], type, 
                    iter = iter, threshold = threshold)
                attr(out, "batch") <- bb
                attr(out, "type") <- attr(out[[1]], 
                    "type")
                attr(out, "threshold") <- threshold
            }
        }
        class(out) <- "QualityScore"
        return(out)
}