R/summary-methods.R

In podkat: Position-Dependent Kernel Association Test

summary.VariantInfo <- function(object, details=FALSE)
{
    if (details)
    {
        cat("Variant info:\n")
        cat("\tNumber of variants:", length(object), "\n\n")

        res <- list(meanMAF=NA, medianMAF=NA, minMAF=NA, maxMAF=NA,
                    tableTypes=NULL)

        if (length(object) > 0)
        {
            MAF <- MAF(object)

            res$meanMAF   <- mean(MAF, na.rm=TRUE)
            res$medianMAF <- median(MAF, na.rm=TRUE)
            res$minMAF    <- min(MAF, na.rm=TRUE)
            res$maxMAF    <- max(MAF, na.rm=TRUE)

            cat("\tMean MAF:   ", res$meanMAF,   "\n")
            cat("\tMedian MAF: ", res$medianMAF, "\n")
            cat("\tMinimum MAF:", res$minMAF,    "\n")
            cat("\tMaximum MAF:", res$maxMAF,    "\n")

            if (length(mcols(object)$type) > 0)
            {
                res$tableTypes <- table(mcols(object)$type, useNA="no")
                n <- sum(res$tableTypes)

                if (n > 0)
                {
                    w1 <- max(nchar(names(res$tableTypes)))
                    w2 <- ceiling(log10(max(res$tableTypes)))

                    labels <- format(paste0(names(res$tableTypes), ":"),
                                     width=(w1 + 2))
                    absNo  <- format(res$tableTypes, justify="right", width=w2)
                    perc   <- format(res$tableTypes * 100 / n, digits=3)

                    cat("\n",
                        paste("\t", labels, absNo, " (", perc, "%)",
                              sep="",collapse="\n"), sep="", "\n")
                }
                else
                    cat("\n\tonly NAs in metadata column 'type'\n")
            }
            else
                cat("\n\tno metadata column 'type' available\n")
        }

        invisible(res)
    }
    else
    {
        object_class <- class(object)
        object_len <- length(object)
        object_mcols <- mcols(object, use.names = FALSE)
        object_nmc <- if (is.null(object_mcols)) 0L else ncol(object_mcols)
        paste0(object_class, " object with ", object_len, " ",
               ifelse(object_len ==  1L, "range", "ranges"), " and ",
               object_nmc, " metadata ",
               ifelse(object_nmc == 1L, "column", "columns"))
    }
}

setMethod("summary", signature(object="VariantInfo"), summary.VariantInfo)