collect-methods {xcms} | R Documentation

## Collect MS$^n$ peaks into xcmsFragments

### Description

Collecting Peaks into `xcmsFragments`s from several MS-runs using `xcmsSet` and `xcmsRaw`.

### Arguments

`object` | (empty) `xcmsFragments-class` object
`xs` | A `xcmsSet-class` object which contains picked ms1-peaks from several experiments
`compMethod` | ("floor", "round", "none"): compare-method which is used to find the parentpeak of a MSnpeak through comparing the MZ-values of the MS1peaks with the MSnParentPeaks.
`snthresh, mzgap, uniq` | these are the paramters for the getspec-peakpicker included in xcmsRaw.

### Details

After running collect(xFragments,xSet) The peaktable of the xcmsFragments includes the ms1Peaks from all experinemts stored in a xcmsSet-object. Further it contains the relevant msN-peaks from the xcmsRaw-objects, which were created temporarily with the paths in xcmsSet.

### Value

A matrix with columns:

`peakID` | unique identifier of every peak
`MSnParentPeakID` | PeakID of the parentpeak of a msLevel>1 - peak, it is 0 if the peak is msLevel 1.
`msLevel` | The msLevel of the peak.
`rt` | retention time of the peak midpoint
`mz` | the mz-Value of the peak
`intensity` | the intensity of the peak
`sample` | the number of the sample from the xcmsSet

### Methods

object = "xcmsFragments"
  `collect(object, ...)`

[Package xcms version 1.14.1 Index]