R/allGenerics.R

In wilsontom/sRm: Toolkit for SRM-MS data (MS) data

#' @rdname plotSRM

setGeneric(
  name = 'plotSRM',
  def = function(object, index, type = 'overlay')
  {
    standardGeneric('plotSRM')
  }
)

#' @rdname plotParent

setGeneric(
  name = 'plotParent',
  def = function(object, parentMass)
  {
    standardGeneric('plotParent')
  }
)

#' @rdname plotSample


setGeneric(
  name = 'plotSample',
  def = function(object, sampleName, polarity)
  {
    standardGeneric('plotSample')
  }
)


#' @rdname smoothChrom

setGeneric(
  name = 'smoothChrom',
  def = function(object, cf)
  {
    standardGeneric('smoothChrom')
  }
)


#' @rdname detectPeaks

setGeneric(
  name = 'detectPeaks',
  def = function(object,
                 snthresh,
                 peakwidth,
                 parallel,
                 cores)
  {
    standardGeneric('detectPeaks')
  }
)


#' @rdname plotPeakArea

setGeneric(
  name = 'plotPeakArea',
  def = function(object, index, sampleName)
  {
    standardGeneric('plotPeakArea')
  }
)


#' @rdname filterPeaks

setGeneric(
  name = 'filterPeaks',
  def = function(object)
  {
    standardGeneric('filterPeaks')
  }
)

#' @rdname peakAsymmetry

setGeneric(
  name = 'peakAsymmetry',
  def = function(object)
  {
    standardGeneric('peakAsymmetry')
  }
)


#' @rdname groupPeaks

setGeneric(
  name = 'groupPeaks',
  def = function(object, rt_tolerance)
  {
    standardGeneric('groupPeaks')
  }
)


#' @rdname transitions

setGeneric(
  name = 'transitions',
  def = function(object)
  {
    standardGeneric('transitions')
  }
)

#' @rdname header

setGeneric(
  name = 'header',
  def = function(object)
  {
    standardGeneric('header')
  }
)

#' @rdname peaks

setGeneric(
  name = 'peaks',
  def = function(object)
  {
    standardGeneric('peaks')
  }
)


#' @rdname meta

setGeneric(
  name = 'meta',
  def = function(object)
  {
    standardGeneric('meta')
  }
)

#' @rdname groupSummary

setGeneric(
  name = 'groupSummary',
  def = function(object)
  {
    standardGeneric('groupSummary')
  }
)


#' @rdname plotGroup

setGeneric(
  name = 'plotGroup',
  def = function(object, group)
  {
    standardGeneric('plotGroup')
  }
)


#' @rdname createGroup

setGeneric(
  name = 'createGroup',
  def = function(object, index, rt, width, id)
  {
    standardGeneric('createGroup')
  }
)


#' @rdname indexRT

setGeneric(
  name = 'indexRT',
  def = function(object, index, sampleName, n)
  {
    standardGeneric('indexRT')
  }
)


#' @rdname keepTransitions

setGeneric(
  name = 'keepTransitions',
  def = function(object, index_keep)
  {
    standardGeneric('keepTransitions')
  }
)


#' @rdname removeTransitions

setGeneric(
  name = 'removeTransitions',
  def = function(object, index_out)
  {
    standardGeneric('removeTransitions')
  }
)




#' @rdname reducePeaks

setGeneric(
  name = 'reducePeaks',
  def = function(object, relative_area)
  {
    standardGeneric('reducePeaks')
  }
)


#' @rdname adjustBaseline

setGeneric(
  name = 'adjustBaseline',
  def = function(object, hwm)
  {
    standardGeneric('adjustBaseline')
  }
)


#' @rdname removeSample

setGeneric(
  name = 'removeSample',
  def = function(object, sampleName)
  {
    standardGeneric('removeSample')
  }
)