R/truePeakTrough.R

In JosieLHayes/adductomicsR: Processing of adductomic mass spectral datasets

#' true peak and trough detection
#' @param peaksTmp character vector with indices of detected peaks
#' from findPeaks
#' @param troughsTmp character vector with indices of detected
#' troughs from findPeaks
#' @param peakRangeTmp matrix of the peak range data with at least
#' 3 columns (1. mass-to-charge, 2. intensity, 3. retention time)
#' @param minRes numeric minimum percentage left/right resolution
#' @param lrRes logical if true both the left and right troughs
#' must be above the minRes else
#' the peak will be discounted. (default = FALSE i.e. if only the
#' left or right trough is less than minRes then the peak will be retained)
#' @usage truePeakTrough(peaksTmp = NULL, troughsTmp = NULL, peakRangeTmp =
#' NULL, minRes = 50, lrRes = FALSE)
#' @return a named numeric of both the peaks and troughs fitting the criteria.
truePeakTrough <- function(peaksTmp = NULL,
                           troughsTmp = NULL,
                           peakRangeTmp = NULL,
                           minRes = 50,
                           lrRes = FALSE) {
    minRes <- 100 / 50
    # identify intra-peak troughs and remove
    truePeaks <- unlist(lapply(seq_along(peaksTmp),
       function(peakInd) {
           # left trough
           nearLTrough <- which(troughsTmp - peaksTmp[peakInd] < 0)
           nearLTrough <-
               nearLTrough[which.min(abs(troughsTmp[nearLTrough] -
                                             peaksTmp[peakInd]))]
           lTroughTmp <- peakRangeTmp[peaksTmp[peakInd], 2] /
               peakRangeTmp[troughsTmp[nearLTrough],  2]
           # right trough
           nearRTrough <- which(troughsTmp - peaksTmp[peakInd] > 0)
           nearRTrough <-
               nearRTrough[which.min(abs(troughsTmp[nearRTrough] -
                                             peaksTmp[peakInd]))]
           rTroughTmp <- peakRangeTmp[peaksTmp[peakInd], 2] /
               peakRangeTmp[troughsTmp[nearRTrough], 2]
           if (lrRes == FALSE) {
               truePeak <- ifelse(lTroughTmp <= minRes & rTroughTmp <=
                                      minRes,
                                  0,
                                  peakInd)
           } else {
               truePeak <- ifelse(lTroughTmp <= minRes | rTroughTmp <=
                                      minRes,
                                  0,
                                  peakInd)
           }
           lTroughTmp <- ifelse(lTroughTmp >= minRes, nearLTrough, 0)
           rTroughTmp <- ifelse(rTroughTmp >= minRes, nearRTrough, 0)
           resTmp <- c(lTroughTmp, truePeak, rTroughTmp)
           names(resTmp) <- c("trough", "peak", "trough")
           return(resTmp)
       }))
    
    truePeaks <- truePeaks[truePeaks != 0]
    return(truePeaks)
}  # end function