R/initialize_peakPantheRAnnotation.R

In peakPantheR: Peak Picking and Annotation of High Resolution Experiments

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## Constructor for \link{peakPantheRAnnotation-class}, initialising a new
## peakPantheRAnnotation with default values, \code{spectraPaths} and
## \code{targetFeatTable} will set the samples and compounds to process
#' @description \code{peakPantheRAnnotation()}: create an instance of the
#' \code{peakPantherAnnotation} class.
#'
#' @param spectraPaths NULL or a character vector of spectra file paths, to set
#' samples to process
#' @param targetFeatTable NULL or a \code{\link{data.frame}} of compounds to
#' target as rows and parameters as columns: \code{cpdID} (str), \code{cpdName}
#' (str), \code{rtMin} (float in seconds), \code{rt} (float in seconds, or
#' \emph{NA}), \code{rtMax} (float in seconds), \code{mzMin} (float), \code{mz}
#' (float or \emph{NA}), \code{mzMax} (float). Set compounds to target.
#' @param cpdID A character vector of compound IDs, of length number of
#' compounds
#' @param cpdName A character vector of compound names, of length number of
#' compounds
#' @param ROI A data.frame of Regions Of Interest (ROI) with compounds as
#' row and ROI parameters as columns: \code{rtMin} (float in seconds), \code{rt}
#' (float in seconds, or \emph{NA}), \code{rtMax} (float in seconds),
#' \code{mzMin} (float), \code{mz} (float or \emph{NA}), \code{mzMax} (float).
#' @param FIR A data.frame of Fallback Integration Regions (FIR) with
#' compounds as row and FIR parameters as columns: \code{rtMin} (float in
#' seconds),
#' \code{rtMax} (float in seconds), \code{mzMin} (float), \code{mzMax} (float).
#' @param uROI A data.frame of updated Regions Of Interest (uROI) with
#' compounds as row and uROI parameters as columns: \code{rtMin} (float in
#' seconds),
#' \code{rt} (float in seconds, or \emph{NA}), \code{rtMax} (float in seconds),
#' \code{mzMin} (float), \code{mz} (float or \emph{NA}), \code{mzMax} (float).
#' @param filepath A character vector of file paths, of length number of spectra
#' files
#' @param cpdMetadata A data.frame of compound metadata, with compounds as row
#' and metadata as columns
#' @param spectraMetadata A data.frame of sample metadata, with samples as row
#' and metadata as columns
#' @param acquisitionTime A character vector of acquisition date-time (converted
#' from POSIXct) or NA
#' @param uROIExist A logical stating if uROI have been set
#' @param useUROI A logical stating if uROI are to be used
#' @param useFIR A logical stating if FIR are to be used
#' @param TIC A numeric vector of TIC or NA, of length number of spectra files
#' @param peakTables A list of peakTable data.frame, of length number of spectra
#' files. Each peakTable data.frame has compounds as rows and peak annotation
#' results as columns.
#' @param dataPoints A list of length number of spectra files. Each list element
#' is a \emph{ROIsDataPoint} list of \code{data.frame} of raw data points for
#' each ROI/uROI (retention time 'rt', mass 'mz' and intensity 'int' (as column)
#' of each raw data points (as row))
#' @param peakFit A list of length number of spectra files. Each list element is
#' a \emph{curveFit} list of \code{peakPantheR_curveFit} or NA for each ROI
#' @param isAnnotated A logical stating in the annotation took place
peakPantheRAnnotation <- function(spectraPaths = NULL,
    targetFeatTable = NULL, cpdID = character(),
    cpdName = character(),
    ROI = data.frame(rtMin = numeric(), rt = numeric(), rtMax = numeric(),
        mzMin = numeric(), mz = numeric(), mzMax = numeric(),
        stringsAsFactors = FALSE),
    FIR = data.frame(rtMin = numeric(), rtMax = numeric(), mzMin = numeric(),
        mzMax = numeric(), stringsAsFactors = FALSE),
    uROI = data.frame(rtMin = numeric(), rt = numeric(), rtMax = numeric(),
        mzMin = numeric(), mz = numeric(), mzMax = numeric(),
        stringsAsFactors = FALSE),
    filepath = character(), cpdMetadata = data.frame(),
    spectraMetadata = data.frame(), acquisitionTime = character(),
    uROIExist = FALSE, useUROI = FALSE, useFIR = FALSE, TIC = numeric(),
    peakTables = list(), dataPoints = list(), peakFit = list(),
    isAnnotated = FALSE) {
    
    # set spectra if spectraPaths is provided
    if (!is.null(spectraPaths)) {
        initSpec <- initialize_spectraPaths(spectraPaths, acquisitionTime, TIC,
                            peakTables, dataPoints, peakFit, spectraMetadata)
        filepath <- initSpec$filepath
        acquisitionTime <- initSpec$acqTime
        TIC <- initSpec$TIC
        peakTables <- initSpec$pkTab
        dataPoints <- initSpec$dataPt
        peakFit <- initSpec$pkFit
        spectraMetadata <- initSpec$specMeta }
    
    # set compounds if targetFeatTable is provided
    if (!is.null(targetFeatTable)) {
        initTarg <- initialize_targetFeatTable(targetFeatTable, cpdMetadata,
                                                FIR, uROI, uROIExist, useUROI)
        cpdID <- initTarg$cpdID
        cpdName <- initTarg$cpdName
        cpdMetadata <- initTarg$cpdMeta
        ROI <- initTarg$ROI
        FIR <- initTarg$FIR
        uROI <- initTarg$uROI
        uROIExist <- initTarg$uROIExist
        useUROI <- initTarg$useUROI }
    
    # set the final values
    new("peakPantheRAnnotation", cpdID = cpdID, cpdName = cpdName, ROI = ROI,
        FIR = FIR, uROI = uROI, filepath = filepath, cpdMetadata = cpdMetadata,
        spectraMetadata = spectraMetadata, acquisitionTime = acquisitionTime,
        uROIExist = uROIExist, useUROI = useUROI, useFIR = useFIR, TIC = TIC,
        peakTables = peakTables, dataPoints = dataPoints, peakFit = peakFit,
        isAnnotated = isAnnotated)
}


# -----------------------------------------------------------------------------
# initialize_peakPantheRAnnotation helper functions

# Set using spectraPaths
initialize_spectraPaths <- function(spectraPaths, acquisitionTime, TIC,
                            peakTables, dataPoints, peakFit, spectraMetadata) {
    # check input is a vector of character
    if (!is.vector(spectraPaths) | is.list(spectraPaths) |
        !is.character(spectraPaths)) {
        stop("specified spectraPaths is not a vector of character") }

    # no duplicated spectraPaths
    if (length(spectraPaths) != length(unique(spectraPaths))) {
        stop("duplicated spectraPaths passed as input") }

    # load values and allocate size
    nbSpectra   <- length(spectraPaths)
    filepath    <- spectraPaths

    # set acquisitionTime default if no acquisitionTime passed in
    if (length(acquisitionTime) == 0) {
        acquisitionTime <- as.character(rep(NA, nbSpectra)) }

    # set TIC default if no TIC passed in
    if (length(TIC) == 0) {
        TIC <- as.numeric(rep(NA, nbSpectra)) }

    # set peakTables default if no peakTables passed in
    if (length(peakTables) == 0) {
        peakTables <- vector("list", nbSpectra) }

    # set dataPoints default if no dataPoints passed in
    if (length(dataPoints) == 0) {
        dataPoints <- vector("list", nbSpectra) }

    # set peakFit default if no peakFit passed in
    if (length(peakFit) == 0) {
        peakFit <- vector("list", nbSpectra) }

    # set spectraMetadata to the correct size if no spectraMetadata passed
    # in (at the correct size)
    if (dim(spectraMetadata)[1] != nbSpectra) {
        spectraMetadata <- data.frame(matrix(, nrow = nbSpectra, ncol = 0))}

    return(list(filepath=filepath, acqTime=acquisitionTime, TIC=TIC,
                pkTab=peakTables, dataPt=dataPoints, pkFit=peakFit,
                specMeta=spectraMetadata))
}
# Set using targetFeatTable
initialize_targetFeatTable <- function(targetFeatTable, cpdMetadata, FIR, uROI,
                                        uROIExist, useUROI){
    # check targetFeatTable
    initialize_checkTargetFeatTable(targetFeatTable)

    # load values and allocate size
    nbCompound  <- dim(targetFeatTable)[1]
    cpdID       <- targetFeatTable$cpdID
    cpdName     <- targetFeatTable$cpdName
    ROI         <- targetFeatTable[, c("rtMin", "rt", "rtMax", "mzMin", "mz",
                                        "mzMax")]
    # set cpdMetadata to the correct size if no cpdMetadata passed in (at the
    # correct size)
    if (dim(cpdMetadata)[1] != nbCompound) {
        cpdMetadata <- data.frame(matrix(, nrow = nbCompound, ncol = 0))
    }
    # only set FIR and uROI to the correct size if not provided in input (at the
    # correct size)
    if (dim(FIR)[1] != nbCompound) {
        FIR <- data.frame(rtMin = as.numeric(rep(NA, nbCompound)),
                            rtMax = as.numeric(rep(NA, nbCompound)),
                            mzMin = as.numeric(rep(NA, nbCompound)),
                            mzMax = as.numeric(rep(NA, nbCompound)),
                            stringsAsFactors = FALSE)
    }
    if (dim(uROI)[1] != nbCompound) {
        uROI <- data.frame(rtMin = as.numeric(rep(NA, nbCompound)),
                            rt = as.numeric(rep(NA, nbCompound)),
                            rtMax = as.numeric(rep(NA, nbCompound)),
                            mzMin = as.numeric(rep(NA, nbCompound)),
                            mz = as.numeric(rep(NA, nbCompound)),
                            mzMax = as.numeric(rep(NA, nbCompound)),
                            stringsAsFactors = FALSE)
        # if we reset, it doesn't exist
        uROIExist <- FALSE
        # if we reset, it can't be used
        useUROI <- FALSE
    }

    return(list(cpdID=cpdID, cpdName=cpdName, cpdMeta=cpdMetadata, ROI=ROI,
                FIR=FIR, uROI=uROI, uROIExist=uROIExist, useUROI=useUROI))
}
# Check targetFeatTable input
initialize_checkTargetFeatTable <- function(targetFeatTable) {

    # check input is data.frame
    if (!is(targetFeatTable, "data.frame")) {
        stop("specified targetFeatTable is not a data.frame")}

    # required columns are present
    if (!all(c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", "mz",
                "mzMax") %in% colnames(targetFeatTable))) {
        stop("expected columns in targetFeatTable are \"cpdID\", ",
            "\"cpdName\", \"rtMin\", \"rt\", \"rtMax\", \"mzMin\", \"mz\" ",
            "and \"mzMax\"")
    }

    # column type
    if (dim(targetFeatTable)[1] != 0) {
        if (!is.character(targetFeatTable$cpdID[1])) {
            stop("targetFeatTable$cpdID must be character") }
        if (!is.character(targetFeatTable$cpdName[1])) {
            stop("targetFeatTable$cpdName must be character") }
        if (!is.numeric(targetFeatTable$rtMin[1])) {
            stop("targetFeatTable$rtMin must be numeric") }
        if (!(is.numeric(targetFeatTable$rt[1]) |
            is.na(targetFeatTable$rt[1]))) {
            stop("targetFeatTable$rt must be numeric or NA") }
        if (!is.numeric(targetFeatTable$rtMax[1])) {
            stop("targetFeatTable$rtMax must be numeric") }
        if (!is.numeric(targetFeatTable$mzMin[1])) {
            stop("targetFeatTable$mzMin must be numeric") }
        if (!(is.numeric(targetFeatTable$mz[1]) |
            is.na(targetFeatTable$mz[1]))) {
            stop("targetFeatTable$mz must be numeric or NA") }
        if (!is.numeric(targetFeatTable$mzMax[1])) {
            stop("targetFeatTable$mzMax must be numeric") }
    }
}