collect-methods {xcms} | R Documentation |
Collecting Peaks into xcmsFragments
s from several
MS-runs using xcmsSet
and
xcmsRaw
.
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. |
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.
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 |
collect(object, ...)