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.
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, ...)
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.