Collect MS^n peaks into xcmsFragments
collect-methods.RdCollecting Peaks into xcmsFragmentss from several
MS-runs using xcmsSet and
xcmsRaw.
Arguments
- object
(empty)
xcmsFragments-classobject- xs
A
xcmsSet-classobject 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