peakDetection {metaMS} | R Documentation

## 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

[Package metaMS version 1.20.0 Index]