featureSpectra: Extract (MS2) spectra associated with features
In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

featureSpectra

R Documentation

Extract (MS2) spectra associated with features

Description

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

Usage

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

Arguments

`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`.

Details

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.

Value

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.