collect-methods: Collect MS^n peaks into xcmsFragments

In yclement/xcms: LC-MS and GC-MS Data Analysis

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 parent peak of a MSnpeak through comparing the MZ-values of the MS1peaks with the MSnParentPeaks.
snthresh, mzgap, uniq	these are the parameters for the getspec-peakpicker included in xcmsRaw.

Details

After running collect(xFragments,xSet) The peak table of the xcmsFragments includes the ms1Peaks from all experiments 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 parent peak 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
GroupPeakMSn	Used for grouped xcmsSet groups
CollisionEnergy	The collision energy of the fragment

Methods

object = "xcmsFragments"

collect(object, ...)

yclement/xcms documentation built on April 10, 2020, 12:08 a.m.