estimatePrecursorIntensity: Estimate precursor intensity for MS level 2 spectra
In sneumann/xcms: LC-MS and GC-MS Data Analysis

estimatePrecursorIntensity,MsExperiment-method

R Documentation

Estimate precursor intensity for MS level 2 spectra

Description

estimatePrecursorIntensity() determines the precursor intensity for a MS 2 spectrum based on the intensity of the respective signal from the neighboring MS 1 spectra (i.e. based on the peak with the m/z matching the precursor m/z of the MS 2 spectrum). Based on parameter method either the intensity of the peak from the previous MS 1 scan is used (method = "previous") or an interpolation between the intensity from the previous and subsequent MS1 scan is used (method = "interpolation", which considers also the retention times of the two MS1 scans and the retention time of the MS2 spectrum).

Usage

## S4 method for signature 'MsExperiment'
estimatePrecursorIntensity(
  object,
  ppm = 10,
  tolerance = 0,
  method = c("previous", "interpolation"),
  BPPARAM = bpparam()
)

## S4 method for signature 'OnDiskMSnExp'
estimatePrecursorIntensity(
  object,
  ppm = 10,
  tolerance = 0,
  method = c("previous", "interpolation"),
  BPPARAM = bpparam()
)

Arguments

`object`	`MsExperiment`, `XcmsExperiment`, `OnDiskMSnExp` or `XCMSnExp` object.
`ppm`	`numeric(1)` defining the maximal acceptable difference (in ppm) of the precursor m/z and the m/z of the corresponding peak in the MS 1 scan.
`tolerance`	`numeric(1)` with the maximal allowed difference of m/z values between the precursor m/z of a spectrum and the m/z of the respective ion on the MS1 scan.
`method`	`character(1)` defining the method how the precursor intensity should be determined (see description above for details). Defaults to `method = "previous"`.
`BPPARAM`	parallel processing setup. See `bpparam()` for details.

Value

numeric with length equal to the number of spectra in x. NA is returned for MS 1 spectra or if no matching peak in a MS 1 scan can be found for an MS 2 spectrum