chromPeakSpectra {xcms} | R Documentation |
Extract (MS2) spectra associated with chromatographic peaks
Description
Extract (MS2) spectra from an XCMSnExp object that represent ions within
the rt and m/z range defined by each chromatographic peak (in the same file
/sample in which the peak was detected).
Usage
chromPeakSpectra(x, msLevel = 2L, expandRt = 0, expandMz = 0,
ppm = 0, method = c("all", "closest_rt", "closest_mz", "signal"),
skipFilled = FALSE, return.type = c("Spectra", "list"))
Arguments
x |
XCMSnExp object with identified chromatographic peaks.
|
msLevel |
integer(1) defining whether MS1 or MS2 spectra should be
returned. Currently only msLevel = 2 is supported.
|
expandRt |
numeric(1) to expand the retention time range of each
peak by a constant value on each side.
|
expandMz |
numeric(1) to expand the m/z range of each peak by a
constant value on each side.
|
ppm |
numeric(1) to expand the m/z range of each peak (on each side)
by a value dependent on the peak's m/z.
|
method |
character(1) specifying which MS2 spectra should be included.
Defaults to "all" in which all MS2 spectra within the rt and m/z range
of a chromatographic peak are returned. "closest_rt" returns the one
MS2 spectrum with the retention time closest to the chromatographic
peak's apex rt. "closest_mz" returns the MS2 spectrum with the
precursor m/z closest to the chromatographic peak's m/z. "signal"
returns the MS2 spectrum which total signal is closest to the
chromatographic peak's maximal signal ("maxo" ).
|
skipFilled |
logical(1) whether no spectra for filled-in peaks should
be reported.
|
return.type |
character(1) defining whether the result should be a
Spectra object or a simple list . See below for more information.
|
Value
Which object is returned depends on the value of return.type
:
For return.type = "Spectra"
: a Spectra object with elements being
Spectrum objects. The result objects contains all spectra that
for all peaks. Metadata column "peak_id"
provides the ID of the
respective peak (i.e. its rowname in chromPeaks).
If return.type = "list"
: list
of list
s 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 peaks.
Author(s)
Johannes Rainer
[Package
xcms version 3.4.4
Index]