MS Data Analysis

Description Usage Arguments Details Value Author(s)

Return (MS2) spectra for all chromatographic peaks associated with the features in x (defined by featureDefinitions()).

1 2	featureSpectra(x, msLevel = 2, expandRt = 0, expandMz = 0, ppm = 0, skipFilled = FALSE, return.type = c("Spectra", "list"), ...)

`x`	XCMSnExp object with feature defitions available.
`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.
`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.
`...`	additional arguments to be passed along to `chromPeakSpectra()`, such as `method`.

The function identifies all MS2 spectra with their precursor m/z within the m/z range of a chromatographic peak of a feature and their retention time within the rt range of the same peak.

The optional parameter method allows to ensure that for each chromatographic peak in one sample only one MS2 spectrum is returned. See chromPeakSpectra() for more details.

Which object is returned depends on the value of return.type:

For return.type = "Spectra" (the default): a Spectra 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, orNULL' if none are present.