featureSpectra: Extract spectra associated with features

In sneumann/xcms: LC-MS and GC-MS Data Analysis

Extract spectra associated with features

Description

This function returns spectra associated with the identified features in the input object. By default, spectra are returned for all features (from all MS levels), but parameter features allows to specify selected features for which the result should be returned. Parameter msLevel allows to define whether MS level 1 or 2 spectra should be returned. For msLevel = 1L all MS1 spectra within the retention time range of each chromatographic peak (in that respective data file) associated with a feature are returned. Note that for samples in which no peak was identified (or even filled-in) no spectra are returned. For msLevel = 2L all MS2 spectra with a retention time within the retention time range and their precursor m/z within the m/z range of any chromatographic peak of a feature are returned. See also chromPeakSpectra() (used internally to extract spectra for each chromatographic peak of a feature) for additional information.

In contrast to the chromPeakSpectra() function, selecting a method different than "all" will not return a single spectrum per feature, but one spectrum per chromatographic peak assigned to the feature.

Note also that msLevel = 1L is only supported for return.type = "List" or return.type = "Spectra".

Usage

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

Arguments

x	XCMSnExp object with feature defitions available.
msLevel	integer(1) defining whether MS1 or MS2 spectra should be returned. msLevel = 1 is currently only supported for return.type being "Spectra" or "List".
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 spectra for filled-in peaks should be reported or not.
return.type	character(1) defining the result type. Defaults to return.type = "MSpectra" but return.type = "Spectra" or return.type = "List" are preferred. See below for more information.
features	character, logical or integer allowing to specify a subset of features in featureDefinitions for which spectra should be returned (providing either their ID, a logical vector same length than nrow(featureDefinitions(x)) or their index in featureDefinitions(x)). This parameter overrides skipFilled and is only supported for return.type being either "Spectra" or "List".
...	additional arguments to be passed along to chromPeakSpectra(), such as method.

Value

parameter return.type allow to specify the type of the returned object:

• return.type = "MSpectra": a MSpectra object with elements being Spectrum objects. The result objects contains all spectra for all features. Metadata column "feature_id" provides the ID of the respective feature (i.e. its rowname in featureDefinitions()).

• return.type = "Spectra": a Spectra object (defined in the Spectra package). The result contains all spectra for all features. Metadata column "feature_id" provides the ID of the respective feature (i.e. its rowname in featureDefinitions().

• return.type = "list": list of lists 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 features.

• return.type = "List": List of length equal to the number of features with MS level msLevel is returned with elements being either NULL (no spectrum found) or a Spectra object.

Author(s)

Johannes Rainer

sneumann/xcms documentation built on March 18, 2023, 6:24 p.m.