generateMSPeakListsMzR: Generate peak lists with mzR

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

Generate peak lists with mzR

Description

Uses the mzR package to read the MS data needed for MS peak lists.

Usage

generateMSPeakListsMzR(fGroups, ...)

## S4 method for signature 'featureGroups'
generateMSPeakListsMzR(
  fGroups,
  maxMSRtWindow = 5,
  precursorMzWindow = 4,
  topMost = NULL,
  avgFeatParams = getDefAvgPListParams(),
  avgFGroupParams = getDefAvgPListParams()
)

## S4 method for signature 'featureGroupsSet'
generateMSPeakListsMzR(fGroups, ...)

Arguments

fGroups	The featureGroups object from which MS peak lists should be extracted.
...	\setsWF Further arguments passed to the non-sets workflow method.
maxMSRtWindow	Maximum chromatographic peak window used for spectrum averaging (in seconds, +/- retention time). If NULL all spectra from a feature will be taken into account. Lower to decrease processing time.
precursorMzWindow	The m/z window (in Da) to find MS/MS spectra of a precursor. This is typically used for Data-Dependent like MS/MS data and should correspond to the isolation m/z window (i.e. +/- the precursor m/z) that was used to collect the data. For Data-Independent MS/MS experiments, where precursor ions are not isolated prior to fragmentation (e.g. bbCID, MSe, all-ion, ...) the value should be NULL.
topMost	Only extract MS peak lists from a maximum of topMost analyses with highest intensity. If NULL all analyses will be used.
avgFeatParams	Parameters used for averaging MS peak lists of individual features. Analogous to avgFGroupParams.
avgFGroupParams	A list with parameters used for averaging of peak lists for feature groups. See getDefAvgPListParams for more details.

Details

This function uses mzR to generate MS peak lists. This function is called when calling generateMSPeakLists with algorithm="mzr".

The MS data files should be either in ‘.mzXML’ or ‘.mzML’ format.

The input MS data files need to be centroided. The convertMSFiles function can be used to centroid data.

Value

A MSPeakLists object.

References

\addCitations

mzR

See Also

generateMSPeakLists for more details and other algorithms.

rickhelmus/patRoon documentation built on July 4, 2025, 9:26 p.m.