View source: R/functions-XCMSnExp.R
This function returns spectra associated with the identified features in the
input object. By default, spectra are returned for all features (from all
MS levels), but parameter
features allows to specify selected features for
which the result should be returned.
msLevel allows to define whether MS level 1 or 2
spectra should be returned. For
msLevel = 1L all MS1 spectra within the
retention time range of each chromatographic peak (in that respective data
file) associated with a feature are returned. Note that for samples in which
no peak was identified (or even filled-in) no spectra are returned.
msLevel = 2L all MS2
spectra with a retention time within the retention time range and their
precursor m/z within the m/z range of any chromatographic peak of a feature
are returned. See also
chromPeakSpectra() (used internally to extract
spectra for each chromatographic peak of a feature) for additional
In contrast to the
chromPeakSpectra() function, selecting a
"all" will not return a single spectrum per feature, but
one spectrum per chromatographic peak assigned to the feature.
Note also that
msLevel = 1L is only supported for
return.type = "List"
return.type = "Spectra".
featureSpectra( x, msLevel = 2L, expandRt = 0, expandMz = 0, ppm = 0, skipFilled = FALSE, return.type = c("MSpectra", "Spectra", "list", "List"), features = character(), ... )
XCMSnExp object with feature defitions available.
additional arguments to be passed along to
return.type allow to specify the type of the returned object:
return.type = "MSpectra": a MSpectra object with elements being
Spectrum objects. The result objects contains all spectra
for all features. Metadata column
"feature_id" provides the ID of the
respective feature (i.e. its rowname in
return.type = "Spectra": a
Spectra object (defined in the
package). The result contains all spectra for all features. Metadata column
"feature_id" provides the ID of the respective feature (i.e. its rowname
return.type = "list":
lists that are either of length
0 or contain Spectrum2 object(s) within the m/z-rt range. The
length of the list matches the number of features.
return.type = "List":
List of length equal to the number of
features with MS level
msLevel is returned with elements being either
NULL (no spectrum found) or a
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