R/print.cnv.R

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

print.cnv <- function(x, digits = 4, ...) {
        cat("\n")
        if (!is.null(attr(x, "mixture"))) {
            cat("Inferred copy number variant by a quantitative signal\n")
            if (is.null(attr(x, "batches"))) 
                cat("   Method:", attr(x, "mixture")$method, " \n\n") 
            else 
                cat("   Method:", attr(x, "mixture")[[1]]$method, " \n\n")
        } else {
            cat("-. Copy number variant\n   Input data: called 
            probabilities\n")
        }
        cat("-. Number of individuals:", length(x), 
            "\n")
        cat("-. Copies", paste(attr(x, "num.copies"), 
            collapse = ", "), "\n")
        if (!is.null(attr(x, "means"))) {
            means <- attr(x, "means")
            if (is.vector(means)) 
                cat("-. Estimated means:", paste(round(attr(x, 
                    "means"), digits = digits), 
                    collapse = ", "), "\n") else {
                colnames(means) <- paste("CNV", 
                    attr(x, "num.copies"))
                cat("-. Estimated means:\n")
                print(round(means, digits = digits))
            }
        }
        if (!is.null(attr(x, "sds"))) {
            sds <- attr(x, "sds")
            if (is.vector(sds)) 
                cat("-. Estimated variances:", 
                    paste(round(attr(x, "sds")^2, 
                    digits = digits), collapse = ", "), 
                    "\n") else {
                colnames(sds) <- paste("CNV", 
                    attr(x, "num.copies"))
                cat("-. Estimated variances:\n")
                print(round(sds^2, digits = digits))
            }
        }
        probs <- colMeans(attr(x, "probabilities"))
        cat("-. Estimated proportions:", paste(round(probs, 
            digits = digits), collapse = ", "), 
            "\n")
        if (!is.null(attr(x, "mixture"))) {
            if (is.null(attr(x, "batches"))) {
                if (!is.null(attr(x, "mixture")$P)) 
                    cat("-. Goodness-of-fit test: p-value=", 
                    attr(x, "mixture")$P, "\n")
            } else {
                if (!is.null(attr(x, "mixture")[[1]]$P)) {
                    cat("-. Goodness-of-fit test:\n")
                    p.values <- cbind(unlist(lapply(attr(x, 
                    "mixture"), function(mixture.i) mixture.i$P)))
                    rownames(p.values) <- paste("Batch", 
                    unique(attr(x, "batches")))
                    colnames(p.values) <- "p-value"
                    print(p.values)
                }
            }
        }
        if (length(attr(x, "copynum.range")) > 
            1) {
            if (!is.null(attr(x, "mixture"))) 
                cat("\n\n-. Note: number of classes has 
            been selected using the best BIC\n")
        }
}