R/print.summary.CNVassoc.R

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

print.summary.CNVassoc <- function(x, digits = max(3, 
        getOption("digits") - 3), ...) {
        cat("\nCall:\n")
        cat(paste(deparse(x$call), sep = "\n", 
            collapse = "\n"), "\n\n", sep = "")
        cat("Deviance:", x$deviance, "\n")
        cat("Number of parameters:", x$numparam, 
            "\n")
        cat("Number of individuals:", length(x$y), 
            "\n")
        cat("\nCoefficients:\n")
        coefs <- x$coefficients
        printCoefmat(coefs, digits = digits, 
            na.print = "", ...)
        family <- attr(x, "family")
        if (family %in% c("binomial", "poisson")) 
            cat("\n(Dispersion parameter for ", 
                family, " family taken to be ", 
                1, ")
            \n\n")
        if (family %in% c("gaussian")) 
            cat("\n(Dispersion parameter estimation for ", 
                family, "family is", format(x$sigma^2), 
                ")\n\n")
        if (family %in% c("weibull")) 
            cat("\n(Shape parameter (alpha) estimation for ", 
                family, "family is", format(x$alpha), 
                ")\n\n")
        if (!family %in% c("gaussian", "binomial", 
            "poisson", "weibull")) 
            stop("Family not implemented: it must be 'gaussian', 'binomial', 
            'poisson' or 'weibull'")
        Varmat <- x$varmat
        p <- NCOL(Varmat)
        cat("\nCovariance between coefficients:\n")
        Varmat <- format(round(Varmat, digits), 
            nsmall = digits, digits = digits)
        Varmat[lower.tri(Varmat)] <- ""
        if (family == "gaussian") 
            Varmat <- Varmat[-p, -p]
        print(Varmat, quote = FALSE)
        cat("\n")
}