R/removePeptides.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 changePearson option to change the peasrson threshold cut-off parameter
#' @param removePeps boolean value indicating whether peptide removal should take place
#'
#' @return  object of class ChemoProtSet
#' @seealso \code{\link{DoschedaSet}}
#' 
#' @export
#' @docType methods
#' @rdname removePeptides-methods
#' @examples
#' \dontrun{
#' 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
#'}

setGeneric(name = "removePeptides", def = function(x, changePearson = NA, removePeps = TRUE) {
    standardGeneric("removePeptides")
})
#' @rdname removePeptides-methods
#' @aliases removePeptides,ANY,ANY-method
#'
setMethod(f = "removePeptides", signature = "ChemoProtSet", definition = function(x, changePearson = NA, 
    removePeps = TRUE) {
    if (!is.na(changePearson)) {
        x@parameters$pearsonThrsh <- changePearson
    }
    
    if (removePeps == FALSE) {
        x@parameters$removePeps <- FALSE
    }
    x@normData <- remove_peptides(dataFrame = x@input, chans = x@parameters$chans, reps = x@parameters$reps, 
        accessionID = "Accession", chanNames = x@parameters$chanNames, sequenceID = "Sequence", qualityID = "Quality", 
        incPDofPD = x@parameters$incPDofPD, PDofPD = "pdofpd", removePeptides = x@parameters$removePeps, 
        modelType = x@parameters$modelType, incGeneFile = x@parameters$incGeneFile, geneFile = x@datasets$GeneID)
    return(x)
})