mzR (version 2.6.2)

mzR-class: Class mzR and sub-classes

Description

The class mzR is the main class for the common mass spectrometry formats. It is a virtual class and thus not supposed to be instanciated directly.

The sub-classes implement specific APIs to access the underlying data and metadata in the files. Currently, mzRramp and mzRpwiz are available implementations. mzRramp uses the ISB 'RAMP' random access C/C++ API, and mzRpwiz uses Proteowizard to access the relevant information in mzData, mzXML and mzML files. You can also open mz5 file by using mzRpwiz.

Additional sub-classes using the proteowizard API and netCDF are planned.

Objects from the Class

mzR is a virtual class, so instances cannot be created.

Objects can be created by calls of the form new("mzRramp", ...), but more often they will be created with openMSfile. After creating a mzR, you can write it into a file. mzXML, mzML, mgf formats are supported.

Extends

Class "Versioned", directly.

References

RAMP: http://tools.proteomecenter.org/wiki/index.php?title=Software:RAMP Proteowizard: http://proteowizard.sourceforge.net/

Examples

library(msdata)
 filepath <- system.file("microtofq", package = "msdata")
 file <- list.files(filepath, pattern="MM14.mzML",
                     full.names=TRUE, recursive = TRUE)
 mzml <- openMSfile(file)
 close(mzml)

 ## using the pwiz backend
 mzml <- openMSfile(file, backend = "pwiz")