featureSpectra {xcms} | 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` list`of [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.

### Author(s)

Johannes Rainer

[Package xcms version 3.10.2 Index]