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Collecting Peaks into xcmsFragmentss from several MS-runs using xcmsSet and xcmsRaw.

Methods

object = "xcmsFragments"

collect(object, ...)

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