Aggregating and combining mass peaks data

In addition to aggregating content of spectra variables (describe in combineSpectra()) it is also possible to aggregate and combine mass peaks data from individual spectra within a Spectra. These combinePeaks() function combines mass peaks within each spectrum with a difference in their m/z values that is smaller than the maximal acceptable difference defined by ppm and tolerance. Parameters intensityFun and mzFun allow to define functions to aggregate the intensity and m/z values for each such group of peaks. With weighted = TRUE (the default), the m/z value of the combined peak is calculated using an intensity-weighted mean and parameter mzFun is ignored. The MsCoreUtils::group() function is used for the grouping of mass peaks. Parameter msLevel. allows to define selected MS levels for which peaks should be combined. This function returns a Spectra with the same number of spectra than the input object, but with possibly combined peaks within each spectrum. Additional peak variables (other than "mz" and "intensity") are dropped (i.e. their values are replaced with NA) for combined peaks unless they are constant across the combined peaks. See also reduceSpectra() for a function to select a single representative mass peak for each peak group.

Usage

# S4 method for class 'Spectra'
combinePeaks(
  object,
  tolerance = 0,
  ppm = 20,
  intensityFun = base::mean,
  mzFun = base::mean,
  weighted = TRUE,
  msLevel. = uniqueMsLevels(object),
  ...
)

Arguments

object: A Spectra object.
tolerance: numeric(1) allowing to define a constant maximal accepted difference between m/z values for peaks to be grouped. Default is tolerance = 0.
ppm: numeric(1) defining a relative, m/z-dependent, maximal accepted difference between m/z values for peaks to be grouped. Default is ppm = 20.
intensityFun: Function to aggregate intensities for all peaks in each peak group into a single intensity value.
mzFun: Function to aggregate m/z values for all mass peaks within each peak group into a single m/z value. This parameter is ignored if weighted = TRUE (the default).
weighted: logical(1) whether m/z values of peaks within each peak group should be aggregated into a single m/z value using an intensity-weighted mean. Defaults to weighted = TRUE.
msLevel.: integer defining the MS level(s) of the spectra to which the function should be applied (defaults to all MS levels of object.
...: ignored.

Author

Sebastian Gibb, Johannes Rainer, Laurent Gatto

Examples


## Create a Spectra from mzML files and use the `MsBackendMzR` on-disk
## backend.
sciex_file <- dir(system.file("sciex", package = "msdata"),
    full.names = TRUE)
sciex <- Spectra(sciex_file, backend = MsBackendMzR())

## Combine mass peaks per spectrum with a difference in their m/z value
## that is smaller than 20 ppm. The intensity values of such peaks are
## combined by summing their values, while for the m/z values the median
## is reported
sciex_comb <- combinePeaks(sciex, ppm = 20,
    intensityFun = sum, mzFun = median)

## Comparing the number of mass peaks before and after aggregation
lengths(sciex) |> head()
#> [1]  578 1529 1600 1664 1417 1602
lengths(sciex_comb) |> head()
#> [1] 149 366 379 374 344 378

## Plotting the first spectrum before and after aggregation
par(mfrow = c(1, 2))
plotSpectra(sciex[2L])
plotSpectra(sciex_comb[2L])


## Using `reduceSpectra()` to keep for each group of mass peaks with a
## difference in their m/z values < 20ppm the one with the highest intensity.
sciex_red <- reduceSpectra(sciex, ppm = 20)

## Comparing the number of mass peaks before and after the operation
lengths(sciex) |> head()
#> [1]  578 1529 1600 1664 1417 1602
lengths(sciex_red) |> head()
#> [1] 149 366 379 374 344 378