R/20.UTR3eSet-class.R

In haibol2016/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

#' UTR3eSet-class and its methods
#'
#' An object of class [UTR3eSet-class] representing the results of 3' UTR usage;
#' methods for constructing, showing, getting and setting attributes of objects;
#' methods for coercing object of other class to [UTR3eSet-class] objects.
#'
#' @section Objects from the Class:
#' Objects can be created by calls of the form \code{new("UTR3eSet", ...)}
#'
#' @section Slots:
#' \describe{
#'    \item{\code{usage}}{Object of class \code{"GRanges"}}
#'    \item{\code{PDUI}}{Object of class \code{"matrix"}}
#'    \item{\code{PDUI.log2}}{Object of class \code{"matrix"}}
#'    \item{\code{short}}{Object of class \code{"matrix"}}
#'    \item{\code{long}}{Object of class \code{"matrix"}}
#'    \item{\code{signals}}{Object of class \code{"list"}}
#'    \item{\code{testRes}}{Object of class \code{"matrix"}}
#' }
#'
#' @section UTR3eSet-class methods:
#' \describe{
#'    \item{$}{\code{signature(x = "UTR3eSet")}: ... }
#'    \item{$<-}{\code{signature(x = "UTR3eSet")}: ... }
#'    \item{coerce}{\code{signature(from = "UTR3eSet", to = "ExpressionSet")}: ... }
#'    \item{coerce}{\code{signature(from = "UTR3eSet", to = "GRanges")}: ... }
#'    \item{show}{\code{signature(object = "UTR3eSet")}: ... }
#' }
#'
#' @name UTR3eSet-class
#' @aliases UTR3eSet-class $,UTR3eSet-method $<-,UTR3eSet-method
#' coerce,UTR3eSet,ExpressionSet-method coerce,UTR3eSet,GRanges-method
#' show,UTR3eSet-method
#' @docType class
#' @section Objects from the Class: Objects can be created by calls of the form
#' \code{new("UTR3eSet", ...)}.
#' @author Jianhong Ou
#' @seealso \code{\linkS4class{GRanges}}
#' @export
#' @author Jianhong Ou

setClass(
  "UTR3eSet",
  representation(
    usage = "GRanges", PDUI = "matrix",
    PDUI.log2 = "matrix",
    short = "matrix",
    long = "matrix",
    signals = "list",
    testRes = "matrix"
  )
)

UTR3eSet <- function(...) {
  new("UTR3eSet", ...)
}

setMethod("$", "UTR3eSet", function(x, name) slot(x, name))

setReplaceMethod(
  "$", "UTR3eSet",
  function(x, name, value) {
    slot(x, name, check = TRUE) <- value
    x
  }
)

setAs(from = "UTR3eSet", to = "ExpressionSet", function(from) {
  ExpressionSet(
    assayData = from$PDUI.log2,
    featureData = AnnotatedDataFrame(as.data.frame(from$usage))
  )
})

setAs(from = "UTR3eSet", to = "GRanges", function(from) {
  n <- from$usage$transcript
  short <- from$short
  long <- from$long
  colnames(short) <- paste(colnames(short), "short.form.usage", sep = "_")
  colnames(long) <- paste(colnames(long), "long.form.usage", sep = "_")
  PDUI <- from$PDUI
  colnames(PDUI) <- paste(colnames(PDUI), "PDUI", sep = "_")

  r <- from$usage
  mcol_r <- as.data.frame(mcols(r))

  if (length(from$testRes) != 0) {
    test <- from$testRes
    mcols(r) <- cbind(
      mcol_r,
      short[match(n, rownames(short)), , drop = FALSE],
      long[match(n, rownames(long)), , drop = FALSE],
      PDUI[match(n, rownames(short)), , drop = FALSE],
      test[match(n, rownames(test)), , drop = FALSE]
    )
  } else {
    mcols(r) <- cbind(
      mcol_r,
      short[match(n, rownames(short)), , drop = FALSE],
      long[match(n, rownames(long)), , drop = FALSE],
      PDUI[match(n, rownames(short)), , drop = FALSE]
    )
  }
  r
})

setMethod("show", "UTR3eSet", function(object) {
  cat("This is an object of UTR3eSet\n", "slot usage:\n")
  show(object$usage)
  if (length(object$PDUI) > 0) {
    cat(
      "slot PDUI: matrix object with ", nrow(object$PDUI),
      " rows ", ncol(object$PDUI), "columns\n"
    )
    show(head(object$PDUI))
    cat("...\n")
    cat(
      "slot PDUI.log2: matrix object with ", nrow(object$PDUI.log2),
      " rows ", ncol(object$PDUI.log2), "columns\n"
    )
    show(head(object$PDUI.log2))
    cat("...\n")
    cat(
      "slot short: matrix object with ", nrow(object$short),
      " rows ", ncol(object$short), "columns\n"
    )
    show(head(object$short))
    cat("...\n")
    cat(
      "slot long: matrix object with ", nrow(object$long),
      " rows ", ncol(object$long), "columns\n"
    )
    show(head(object$long))
    cat("...\n")
  }
  if (length(object$signals) > 0) {
    cat("slot signals: length ", length(object$signals), "\n")
  }
  if (length(object$testRes) > 0) {
    cat(
      "slot testRes: matrix object with ", nrow(object$testRes),
      " rows ", ncol(object$testRes), "columns\n"
    )
    show(head(object$testRes))
    cat("...\n")
  }
})