xcmsFragments-class {xcms}R Documentation

Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data

Description

This class is similar to xcmsSet because it stores peaks from a number of individual files. However, xcmsFragments keeps Tandem MS and e.g. Ion Trap or Orbitrap MS$^n$ peaks, including the parent ion relationships.

Objects from the Class

Objects can be created with the xcmsFragments constructor and filled with peaks using the collect method.

Slots

peaks:
matrix with colmns peakID (MS1 parent in corresponding xcmsSet), MSnParentPeakID (parent peak within this xcmsFragments), msLevel (e.g. 2 for Tandem MS), rt (retention time in case of LC data), mz (fragment mass-to-charge), intensity (peak intensity as reported by XXX), sample (The ID of the rawData-file).

Methods

collect
signature(object = "xcmsFragments"): gets a xcmsSet-object, collects ms1-peaks from it and the msn-peaks from the corresponding xcmsRaw-files.
plotTree
signature(object = "xcmsFragments"): prints a (text based) pseudo-tree of the peaktable to display the dependencies of the peaks among each other.
show
signature(object = "xcmsFragments"): print a human-readable description of this object to the console.

Note

No notes yet.

Author(s)

S. Neumann, J. Kutzera

References

A parallel effort in metabolite profiling data sharing: http://metlin.scripps.edu/

See Also

xcmsRaw


[Package xcms version 1.14.1 Index]