R/00AdductQuantif-class.R

In JosieLHayes/adductomicsR: Processing of adductomic mass spectral datasets

#' AdductQuantif-class
#' The AdductQuantif-class contains a peak integral matrix,
#' peak ranges and region of integration, the isotopic distribution identified
#' for each integrated peak and the target table of peaks integrated.
#' @include 00AdductSpec-class.R
#' @slot peakQuantTable a matrix containing the peak
#' integration results and
#' consisting of a row for each peak
#' identified in each sample (e.g 200 samples
#' and 50 targets 200 * 50 = 10,000 rows)
#' @slot peakIdData list of peak IDs
#' @slot predIsoDist list of predicted Iso distances
#' @slot targTable dataframe target table
#' @slot file.paths character path to file
#' @slot Parameters dataframe of specified parameters
#' @return peak integral matrix,
#' peak ranges and region of integration, the isotopic distribution identified
#' for each integrated peak and the target table of peaks integrated
#' and their corresponding MS1 scan isotopic patterns
#' @name AdductQuantif class
#' @rdname AdductQuantif class
#' @aliases show,c,AdductQuantif,AdductQuantif-class
#' @exportClass AdductQuantif

#' @author JL Hayes \email{jlhayes1982@gmail.com}
setClass(
    "AdductQuantif",
    representation(
        peakQuantTable = "matrix",
        peakIdData = 'list',
        predIsoDist = 'list',
        targTable = 'data.frame',
        file.paths = "character",
        Parameters = "data.frame"
    )
)
#' @rdname AdductQuantif-class
#' @aliases c,AdductQuantif-method
x <- NULL
setMethod("c", signature(x = "AdductQuantif"), function(x, ...) {
    elements = list(...)
    # error handling check if all adductSpec object
    if (any(vapply(elements, function(ele)
        is(ele, 'AdductQuantif'),
        FUN.VALUE = logical(1)) == FALSE)) {
        stop("all elements must be an
        AdductQuantif class object")
    }
    emptyAdductQuantif <- new("AdductQuantif")
    for (i in seq_along(elements)) {
        if (ncol(emptyAdductQuantif@peakQuantTable==0)
            ) {
            emptyAdductQuantif@peakQuantTable <-
                elements[[i]]@peakQuantTable
        } else {
            emptyAdductQuantif@peakQuantTable <-
                rbind(emptyAdductQuantif@peakQuantTable,
                elements[[i]]@peakQuantTable)
        }
        emptyAdductQuantif@peakIdData <-
            c(emptyAdductQuantif@peakIdData,
            elements[[i]]@peakIdData)
        emptyAdductQuantif@predIsoDist <-
            c(emptyAdductQuantif@predIsoDist,
            elements[[i]]@predIsoDist)
        # keep unique
        emptyAdductQuantif@predIsoDist <-
            emptyAdductQuantif@predIsoDist[!duplicated(names(
                emptyAdductQuantif@predIsoDist))]
        # target table
        emptyAdductQuantif@targTable <-
            rbind(emptyAdductQuantif@targTable,
                elements[[i]]@targTable)
        # remove duplicates
        uniEntries <-
            apply(emptyAdductQuantif@targTable[, seq_len(3)],
                1, paste, collapse = "")
        emptyAdductQuantif@targTable <-
            emptyAdductQuantif@targTable[duplicated(uniEntries) ==
                                            FALSE, , drop = FALSE]
        emptyAdductQuantif@file.paths <-
            c(emptyAdductQuantif@file.paths,
            elements[[i]]@file.paths)
    }
    return(emptyAdductQuantif)
    })  # end function
setGeneric("file.paths", function(object)
    standardGeneric("file.paths"))
setMethod(
    "file.paths",
    signature = "AdductQuantif",
    definition = function(object) {
        return(object@file.paths)
    }
)
setGeneric("file.paths<-", function(object,
                                    value)
    standardGeneric("file.paths<-"))
setMethod("file.paths<-", "AdductQuantif", function(object, value) {
    object@file.paths <- value
    if (validObject(object))
        return(object)
})

setGeneric("peakQuantTable", function(object)
    standardGeneric("peakQuantTable"))
setMethod(
    "peakQuantTable",
    signature = "AdductQuantif",
    definition = function(object) {
        return(object@peakQuantTable)
    }
)
setGeneric("peakQuantTable<-", function(object,
                                        value)
    standardGeneric("peakQuantTable<-"))
setMethod("peakQuantTable<-", "AdductQuantif", function(object, value) {
    object@peakQuantTable <- value
    if (validObject(object))
        return(object)
})

setGeneric("peakIdData", function(object)
    standardGeneric("peakIdData"))
setMethod(
    "peakIdData",
    signature = "AdductQuantif",
    definition = function(object) {
        return(object@peakIdData)
    }
)
setGeneric("peakIdData<-", function(object,
                                    value)
    standardGeneric("peakIdData<-"))
setMethod("peakIdData<-", "AdductQuantif", function(object, value) {
    object@peakIdData <- value
    if (validObject(object))
        return(object)
})

setGeneric("predIsoDist", function(object)
    standardGeneric("predIsoDist"))
setMethod(
    "predIsoDist",
    signature = "AdductQuantif",
    definition = function(object) {
        return(object@predIsoDist)
    }
)
setGeneric("predIsoDist<-", function(object,
                                    value)
    standardGeneric("predIsoDist<-"))
setMethod("predIsoDist<-", "AdductQuantif", function(object, value) {
    object@predIsoDist <- value
    if (validObject(object))
        return(object)
})

setGeneric("targTable", function(object)
    standardGeneric("targTable"))
setMethod(
    "targTable",
    signature = "AdductQuantif",
    definition = function(object) {
        return(object@targTable)
    }
)
setGeneric("targTable<-", function(object,
                                value)
    standardGeneric("targTable<-"))
setMethod("targTable<-", "AdductQuantif", function(object, value) {
    object@targTable <- value
    if (validObject(object))
        return(object)
})