Defines functions print.cnv

Documented in print.cnv

print.cnv <-
function (x, digits = 4, ...)
    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")$method, " \n\n")
          cat("   Method:", attr(x, "mixture")[[1]]$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 = ", "),
    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")
          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")
          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")
        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")))
    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")

Try the CNVassoc package in your browser

Any scripts or data that you put into this service are public.

CNVassoc documentation built on May 30, 2017, 12:50 a.m.