R/generateIonChromatogram.R

In peakPantheR: Peak Picking and Annotation of High Resolution Experiments

#' Generate ion chromatogram from raw data points
#'
#' On the input raw data, aggregate intensites across the mz range at each retention time to generate an ion chromatogram: \code{sum} for EIC/TIC, \code{max}, \code{min} or \code{mean}. The number of data points returned correspond to the number of unique scans/retention time measurements in the input data
#' @param ROIDataPoint (data.frame) retention time "rt", mass "mz" and intensity "int" (as column) of each raw data points (as row) to use for the ion chromatogram
#' @param aggregationFunction (str) Function to use in order to aggregate intensities across mz in each scan. One of \code{sum}, \code{max}, \code{min}, \code{mean}
#'
#' @return A data.frame of retention time "rt" and aggregated intensities "int"
#' 
#' @examples
#' \dontrun{
#' ## Input data points
#' in_rt   <- c(3362.102, 3362.102, 3363.667, 3363.667, 3365.232, 3365.232, 3366.797, 3366.797,
#'              3368.362, 3368.362)
#' in_mz   <- c(496.2, 497.2, 496.2, 497.2, 496.2, 497.2, 496.2, 497.2, 496.2, 497.2)
#' in_int  <- c(39616, 11432, 63344, 18224, 107352, 30936, 182144, 51776, 295232, 81216)
#' input_ROIDataPoints <- data.frame(rt=in_rt, mz=in_mz, int=in_int)
#'
#' ## Aggregate mz to generate EIC
#' EIC <- generateIonChromatogram(input_ROIDataPoints, aggregationFunction='sum')
#' EIC
#' #         rt    int
#' # 1 3362.102  51048
#' # 2 3363.667  81568
#' # 3 3365.232 138288
#' # 4 3366.797 233920
#' # 5 3368.362 376448
#' }
generateIonChromatogram <- function(ROIDataPoint, aggregationFunction='sum') {
  
  # Check input
  if (class(ROIDataPoint) != 'data.frame') {
    stop('Check input "ROIDataPoint" must be a data.frame')
  } else if (!all(c('rt', 'mz', 'int') %in% colnames(ROIDataPoint))) {
    stop('Check input "ROIDataPoint must have the following columns: "rt", "mz", "int"')
  }
  if (!(aggregationFunction) %in% c('sum', 'mean', 'min', 'max')) {
    stop('Check input "aggregationFunction" must be one of: "sum", "mean", "min", "max"')
  }
  
  # No data to aggregate
  if (dim(ROIDataPoint)[1] == 0) {
    return(data.frame(rt=numeric(), int=numeric()))
  }
  
  # Init
  unique_scans  <- sort(unique(ROIDataPoint$rt))
  res           <- data.frame(matrix(vector(), nrow=length(unique_scans), ncol=2, dimnames=list(c(),c('rt','int'))))
  
  # for each scan, aggregate intensity
  for (i in 1:length(unique_scans)) {
    cur_scan  <- unique_scans[i]
    tmp_int   <- ROIDataPoint[ROIDataPoint$rt == cur_scan, c('int')]
    res[i,]   <- c(cur_scan, do.call(aggregationFunction, list(tmp_int)))
  }
  
  return(res)
}