R/AllMethods.R

In daanhazelaar/katdetectr: Detection, Characterization and Visualization of Kataegis in Sequencing Data

# Accessor methods ----------------------------------------------------------

#' @rdname getGenomicVariants
#' @exportMethod getGenomicVariants
setMethod('getGenomicVariants', 'KatDetect', function(x){ return( x@genomicVariants) })

#' @rdname getSegments
#' @exportMethod getSegments
setMethod('getSegments', 'KatDetect', function(x){ return( x@segments) })

#' @rdname getKataegisFoci
#' @exportMethod getKataegisFoci
setMethod('getKataegisFoci', 'KatDetect', function(x){ return( x@kataegisFoci) })

#' @rdname getInfo
#' @exportMethod getInfo
setMethod('getInfo', 'KatDetect', function(x){return( x@info)})


# summary and show functions ---------------

#' @export
summary.KatDetect <- function(object, ...){
    base::cat("Sample name:                                ", object@info$sampleName, "\n")
    base::cat("Total number of genomic variants:           ", object@info$totalGenomicVariants, "\n")
    base::cat("Total number of putative Kataegis foci:     ", object@info$totalKataegisFoci, "\n")
    base::cat("Total number of variants in a Kataegis foci:", object@info$totalVariantsInKataegisFoci)
}

#' @export
print.KatDetect <- function(x, ...){
    return(summary(x, ...))
}

setMethod("show", "KatDetect", function(object){
    base::cat("Class 'KatDetect' : KatDetect Object\n")
    base::cat("                  : S4 class containing", base::length(base::attributes(object))-1, "slots with names:\n")
    base::cat("                   ", base::names(base::attributes(object))[seq_len(base::length(base::attributes(object)))-1], "\n\n")
    base::cat("Created on:        ", object@info$date, "\n")
    base::cat("katdetectr version:", object@info$version,'\n\n')
    base::cat("summary: \n--------------------------------------------------------\n")
    summary(object)
    base::cat("\n--------------------------------------------------------")
})