MSnExp-class: The 'MSnExp' Class for MS Data And Meta-Data

Description

The MSnExp class encapsulates data and meta-data for mass spectrometry experiments, as described in the slots section. Several data files (currently in mzXML) can be loaded together with the function readMSData.

This class extends the virtual "pSet" class.

In version 1.19.12, the polarity slot had been added to the "Spectrum" class (previously in "Spectrum1"). Hence, "MSnExp" objects created prior to this change will not be valid anymore, since all MS2 spectra will be missing the polarity slot. Object can be appropriately updated using the updateObject method.

Arguments

concept

MSnExp

Objects from the Class

Objects can be created by calls of the form new("MSnExp",...). However, it is preferred to use the readMSData function that will read raw mass spectrometry data to generate a valid "MSnExp" instance.

Extends

Class "pSet", directly. Class "VersionedBiobase", by class "pSet", distance 2. Class "Versioned", by class "pSet", distance 3.

References

Information about the mzXML format as well converters from vendor specific formats to mzXML: http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML.

Examples

Run this code

mzxmlfile <- dir(system.file("extdata",package="MSnbase"),
                 pattern="mzXML",full.names=TRUE)
msnexp <- readMSData(mzxmlfile)
msnexp

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