R/fitModel.R

In brunocontrino/Doscheda: A DownStream Chemo-Proteomics Analysis Pipeline

#' Method to fit a model to an object of class 'ChemoProtSet'
#'
#' @param x object of class 'ChemoProtSet'
#'
#' @return  object of class ChemoProtSet
#' @seealso \code{\link{DoschedaSet}}
#'
#' @export
#' @docType methods
#' @rdname fitModel-methods
#' @examples
#' channelNames <- c('Abundance..F1..126..Control..REP_1',
#''Abundance..F1..127..Sample..REP_1',  'Abundance..F1..128..Sample..REP_1',
#'  'Abundance..F1..129..Sample..REP_1',  'Abundance..F1..130..Sample..REP_1',
#''Abundance..F1..131..Sample..REP_1',  'Abundance..F2..126..Control..REP_2',
#' 'Abundance..F2..127..Sample..REP_2', 'Abundance..F2..128..Sample..REP_2',
#''Abundance..F2..129..Sample..REP_2',  'Abundance..F2..130..Sample..REP_2',
#''Abundance..F2..131..Sample..REP_2')
#' ex <- new('ChemoProtSet')
#' ex<- setParameters(x = ex,chansVal = 6, repsVal = 2,dataTypeStr = 'intensity',
#'  modelTypeStr = 'linear',PDBool = FALSE,removePepsBool = FALSE,
#'  incPDofPDBool = FALSE,incGeneFileBool = FALSE,organismStr = 'H.sapiens', pearsonThrshVal = 0.4)
#' ex<- setData(x = ex, dataFrame = doschedaData, dataChannels = channelNames,
#' accessionChannel = 'Master.Protein.Accessions',
#'               sequenceChannel = 'Sequence', qualityChannel = 'Qvality.PEP' )
#' ex <- removePeptides(ex,removePeps = FALSE)
#' ex <- runNormalisation(ex)
#' ex <- fitModel(ex)
#' ex
#'
setGeneric(name = "fitModel", def = function(x) {
    standardGeneric("fitModel")
})
#' @rdname fitModel-methods
#'
#'@examples
#'ex <- processedExample
#'ex <- runNormalisation(ex)
#'ex <- fitModel(ex)
#'
#'ex
#' @aliases fitModel,ANY,ANY-method
#'
setMethod(f = "fitModel", signature = "ChemoProtSet", definition = function(x) {
    if (dim(x@normData)[1] == 0) {
        x@finalData <- fit_model(dataFrame = x@input, chans = x@parameters$chans, reps = x@parameters$reps, 
            PD2 = x@parameters$PD, sigmoidConc = x@parameters$sigmoidConc, incPDofPD = x@parameters$incPDofPD, 
            PDofPD = x@parameters$PDofPD, dataType = x@parameters$dataType, modelType = x@parameters$modelType)
    } else {
        x@finalData <- fit_model(dataFrame = x@normData, chans = x@parameters$chans, reps = x@parameters$reps, 
            PD2 = x@parameters$PD, sigmoidConc = x@parameters$sigmoidConc, incPDofPD = x@parameters$incPDofPD, 
            PDofPD = x@parameters$PDofPD, dataType = x@parameters$dataType, modelType = x@parameters$modelType)
    }
    
    return(x)
})