peakDetection: Wrapper for XCMS peak detection, to be used for both GC-MS...

In rwehrens/metaMS: MS-based metabolomics annotation pipeline

Wrapper for XCMS peak detection, to be used for both GC-MS and LC-MS data.

Description

XCMS peak detection using settings, defined for individual laboratories and depending on the chromatographic and mass-spectrometric characteristics of the instruments at hand.

Usage

peakDetection(files, settings, rtrange = NULL, mzrange= NULL,
              convert2list = FALSE, nSlaves = 0) 

Arguments

files	input files (including path names) that will be processed by xcms.
settings	a list of settings that will be passed on to the xcmsSet function. See the help of FEMsettings for a detailed description of the fields in this list.
rtrange	If non-NULL, a vector to subset the region of the chromatography retained for further analysis (given in minutes).
mzrange	If non-NULL, a vector indicating the subset of the mass spectrum retained for the analysis.
convert2list	logical. If TRUE, the xcmsSet object will be split into a list of one-sample objects which will be treated separately. This is useful not only in GC-MS data, where peak alignment is avoided, but also in setting up databases of standards, where no common peaks between injections are expected to occur.
nSlaves	Number of cores to be used in the peak picking.

Value

Either an xcmsSet object, or a list of one-sample xcmsSet objects.

Author(s)

Ron Wehrens and Pietro Franceschi

Examples

## Example of settings
  data(FEMsettings)
  metaSetting(object = TSQXLS.GC, field= "PeakPicking")

rwehrens/metaMS documentation built on Feb. 27, 2023, 5:13 a.m.