getPeakTable: Extract a peak table from an xcms or CAMERA object

In metaMS: MS-based metabolomics annotation pipeline

Description

Extracts the peak table (a data.frame) from an xcms (or CAMERA) object (without compound annotation). The peak table contains the mass and retention time for all the features and their intensities across the samples. This function is not meant to be called directly, but it is internally used by runLC, getAnnotationLC, createSTDdbLC.

Usage

getPeakTable(xs, intval = "into")

Arguments

xs	The xcmsSet (or CAMERA) object
intval	The intensity measure extracted form xs.

Details

The function process an xs object and returns for it a PeakTable which associates intensities to features and samples. The default measure for the intensity is into (the chromatographic peak area for a feature), but in the case of annotation, maxo (value for the intensity of the ion over the chromatographic peak) is used to measure the intensity. For a more detailed description of the possible intensity measures refer to the documentation of xcms].

Value

A data frame with the intensity for each feature (rows) in all the samples (columns). Each feature is identified by its m/z value and retention time (in minutes). If the xs object is of class CAMERA, the results of the camera annotation (isotope, adduct, pcgroup) are included in the table.

Author(s)

Pietro Franceschi

Examples

## Example of results
  data(LCresults) ## pre-compiled results
  LCresults$PeakTable

metaMS documentation built on Nov. 8, 2020, 8:21 p.m.