Uses the mzR package to read the MS data needed for MS peak lists.
generateMSPeakListsMzR(fGroups, ...)
# S4 method for class 'featureGroups'
generateMSPeakListsMzR(
fGroups,
maxMSRtWindow = 5,
precursorMzWindow = 4,
topMost = NULL,
avgFeatParams = getDefAvgPListParams(),
avgFGroupParams = getDefAvgPListParams()
)
# S4 method for class 'featureGroupsSet'
generateMSPeakListsMzR(fGroups, ...)The featureGroups object from which MS peak lists should be extracted.
(sets workflow) Further arguments passed to the non-sets workflow method.
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.
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.
Only extract MS peak lists from a maximum of topMost analyses with highest intensity. If
NULL all analyses will be used.
Parameters used for averaging MS peak lists of individual features. Analogous to
avgFGroupParams.
A list with parameters used for averaging of peak lists for feature groups. See
getDefAvgPListParams for more details.
A MSPeakLists object.
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.
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generateMSPeakLists for more details and other algorithms.