R/runNormalisation.R

In Doscheda: A DownStream Chemo-Proteomics Analysis Pipeline

#' Method to remove peptides from input data of an object of class 'ChemoProtSet'
#'
#' @param x object of class 'ChemoProtSet'
#' @param normalise string indicating the type of normalisation that should take place ('loess', 'median', 'none')
#'
#' @return  object of class ChemoProtSet
#' @seealso \code{\link{DoschedaSet}}
#' 
#'@examples
#'ex <- processedExample
#'ex <- runNormalisation(ex)
#'ex
#'
#' @export
#' @docType methods
#' @rdname runNormalisation-methods
setGeneric(name = "runNormalisation", def = function(x, normalise = "loess") {
    standardGeneric("runNormalisation")
})
#' @rdname runNormalisation-methods
#' @aliases runNormalisation,ANY,ANY-method
#'
setMethod(f = "runNormalisation", signature = "ChemoProtSet", definition = function(x, normalise = "loess") {
    if (x@parameters$dataType == "intensity") {
        x@normData <- normalize_data(dataFrame = x@normData, chans = x@parameters$chans, reps = x@parameters$reps, 
            PD2 = x@parameters$PD, channelNames = x@parameters$chanNames, incPDofPD = x@parameters$incPDofPD, 
            PDofPD = "pdofpd", removePeptides = x@parameters$removePeps, dataType = x@parameters$dataType, 
            modelType = x@parameters$modelType, organism = x@parameters$organism, incGeneFile = x@parameters$incGeneFile, 
            normaliseData = normalise)
        
    } else {
        x@normData <- normalize_data(dataFrame = x@input, chans = x@parameters$chans, reps = x@parameters$reps, 
            PD2 = x@parameters$PD, channelNames = x@parameters$chanNames, incPDofPD = x@parameters$incPDofPD, 
            PDofPD = "pdofpd", removePeptides = x@parameters$removePeps, dataType = x@parameters$dataType, 
            modelType = x@parameters$modelType, organism = x@parameters$organism, incGeneFile = x@parameters$incGeneFile, 
            normaliseData = normalise)
    }
    
    return(x)
})