collect-methods {xcms}R Documentation

Collect MS$^n$ peaks into xcmsFragments

Description

Collecting Peaks into xcmsFragmentss 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]