featureSpectra {xcms} | R Documentation |
Return (MS2) spectra for all chromatographic peaks associated with the
features in x
(defined by featureDefinitions()
).
featureSpectra( x, msLevel = 2, expandRt = 0, expandMz = 0, ppm = 0, skipFilled = FALSE, return.type = c("MSpectra", "list"), ... )
x |
XCMSnExp object with feature defitions available. |
msLevel |
|
expandRt |
|
expandMz |
|
ppm |
|
skipFilled |
|
return.type |
|
... |
additional arguments to be passed along to |
The function identifies all MS2 spectra with their precursor m/z within the
m/z range of a chromatographic peak (i.e. >=
mzmin and <=
mzmax) of a
feature and their retention time within the rt range of the same peak
(>=
rtmin and <=
rtmax).
The optional parameter method
allows to ensure that for each
chromatographic peak in one sample only one MS2 spectrum is returned.
See chromPeakSpectra()
or the LC-MS/MS analysis vignette for more
details.
Which object is returned depends on the value of return.type
:
For return.type = "MSpectra"
(the default): a MSpectra object with data
only for features for which a Spectrum2 was found. The
ID of the feature and of the chromatographic peak to which the
spectrum is associated are provided with the "feature_id"
and
"peak_id"
metadata columns.
For return.type = "list"
: a list, same length than there are features in
x, each element being a
listof [Spectrum2-class] objects with the MS2 spectra that potentially represent ions measured by each chromatographic peak associated with the feature, or
NULL'
if none are present.
Johannes Rainer