R/MadSeqMethod.R

In ykong2/MADSEQ: Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

## accessor for MadSeq object
## 1. posterior
#' Accessing posterior distribution of MadSeq object
#' 
#' An S4 method to access the posterior distribution of
#' \code{\link{MadSeq}} object
#' @param object A \code{MadSeq} object returned by \code{\link{runMadSeq}} 
#' function
#' @return A \code{matrix} containing posterior distribution of selected model
#' @examples 
#' ## load the example MadSeq object come with the package
#' data("aneuploidy_chr18")
#' 
#' ## access posterior distribution
#' posterior(aneuploidy_chr18)
#' @seealso \code{\link{MadSeq}}, \code{\link{runMadSeq}}
#' @rdname posterior
#' @author Yu Kong
#' @export
setMethod(
    "posterior",
    signature = "MadSeq",
    definition = function(object){
        object@posterior
    })

## 2. deltaBIC
#' Accessing delta BIC of MadSeq object
#' 
#' An S4 method to access the delta BIC values of \code{\link{MadSeq}} object
#' @param object A \code{MadSeq} object returned by \code{\link{runMadSeq}} 
#' function
#' @return A \code{numeric} vector containing deltaBIC values between selected
#' model and other models
#' @examples 
#' ## load the example MadSeq object come with the package
#' data("aneuploidy_chr18")
#' 
#' ## access deltaBIC 
#' deltaBIC(aneuploidy_chr18)
#' @seealso \code{\link{MadSeq}}, \code{\link{runMadSeq}}
#' @rdname deltaBIC
#' @author Yu Kong
#' @export
setMethod(
    "deltaBIC",
    signature = "MadSeq",
    definition = function(object){
        object@deltaBIC
    })


## summary function for MadSeq object
#' Summarize statistics of the MadSeq object
#' 
#' An S4 method to summarize statistics for \code{\link{MadSeq}} object
#' @param object A \code{MadSeq} object returned by \code{\link{runMadSeq}} 
#' function
#' @return a \code{table} containing statistics for each parameters in the 
#' selected model
#' @examples 
#' ## load the example MadSeq object come with the package
#' data("aneuploidy_chr18")
#' 
#' ## show statistics
#' summary(aneuploidy_chr18)
#' @author Yu Kong
#' @rdname summary-method
#' @aliases summary
#' @export
setMethod(
    "summary",
    signature = "MadSeq",
    definition = function(object){
        model_selected = names(object@deltaBIC)[1]
        model_selected = substr(model_selected,5,nchar(model_selected))
        cat("model selected:",model_selected,"\n")
        summary(object@posterior)
    })

## show method for MadSeq object
setMethod(
    "show",
    signature = "MadSeq",
    definition = function(object){
        model_selected = names(object@deltaBIC)[1]
        model_selected = substr(model_selected,5,nchar(model_selected))
        cat(paste(class(object),
                "object with the posterior distribution from",
                model_selected, "model\n",sep=" "))
        print(head(object@posterior))
        cat("------\n")
        print(object@deltaBIC)
    })