R/convertMsp2Spectra.R

In MetCirc: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data

#' @name convertMsp2Spectra
#'
#' @title Convert MSP data frame into object of class `MSpectra`
#'
#' @description Convert msp data frame into object of class [MSpectra()]
#'
#' @param
#' msp `data.frame` that mimicks the .msp file format, see Details for further
#' information
#'
#' @details
#' msp is a data frame of a .msp file, a typical data file for
#' MS/MS libraries. The data frame has two columns and contains in the first
#' column the entries "NAME:",
#' "PRECURSORMZ:" (or "EXACTMASS:"), "RETENTIONTIME:", Num Peaks:"
#' and information on fragments and peak areas/intensities and will
#' extract the respective information in the second column.
#'
#' @return `convertMsp2Spectra` returns an object of class `MSpectra`
#'
#' @author Thomas Naake, \email{thomasnaake@@googlemail.com}
#'
#' @examples
#' data("convertMsp2Spectra", package = "MetCirc")
#' convertMsp2Spectra(msp = msp2spectra)
#'
#' @export
convertMsp2Spectra <- function(msp) {

    nameInd <- grep("NAME:", msp[, 1]) ## indices of Name

    ## get indices of precursor mz or exactmass
    mzInd_1 <- grep("PRECURSORMZ:", msp[, 1])
    mzInd_2 <- grep("EXACTMASS:", msp[, 1])

    mzInd <- if (length(mzInd_1) >= length(mzInd_2)) {
        mzInd_1
    } else {
        mzInd_2
    }

    numpeaksInd <- grep("Num Peaks:", msp[, 1])

    ## get indices of "RETENTIONTIME:"
    rtInd <- grep("RETENTIONTIME:", msp[, 1])

    NAMES <- as.character(msp[nameInd,  2])
    MZ <- as.numeric(as.character(msp[mzInd, 2]))
    NUMPEAKS <- as.numeric(as.character(msp[numpeaksInd, 2]))

    ## how many entries are in msp
    numEntries <- length(NAMES)

    if (numEntries != length(MZ)) 
        stop("length of precursor mz != length of names")

    ## create annotation vectors
    RT <- if (length(rtInd) == numEntries) {
        as.numeric(as.character(msp[rtInd, 2]))
    } else {
        rep(NaN, numEntries)
    }

    spN_l <- vector("list", numEntries)

    for (i in 1:numEntries) {
        beg <- numpeaksInd[i] + 1
        end <- numpeaksInd[i] + NUMPEAKS[i]
        fragment <- as.numeric(as.character(msp[beg:end, 1]))
        intensity <- as.numeric(as.character(msp[beg:end, 2]))

        ## sort fragments according to increasing fragment values
        fragment <- sort(fragment)
        intensity <- intensity[order(fragment)]

        ## delete double entries
        intensity <- intensity[!duplicated(fragment)]
        fragment <- fragment[!duplicated(fragment)]

        ## calculate percentages
        ##intensity <- intensity / max(intensity) * 100

        spN_l[[i]] <- new("Spectrum2", rt = RT[i], precursorMz = MZ[i],
                         mz = fragment, intensity = intensity)
    }

    spl <- MSpectra(spN_l, elementMetadata = DataFrame(names = NAMES))
    return(spl)
}