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.

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.

Slots

fileName:

Object of class character storing the original filename used when the instance was created.

backend:

One of the implemented backens or NULL.

.__classVersion__:

Object of class "Versioned", from Biobase.

Extends

Class "Versioned", directly.

Methods

For methods to access raw data (spectra and chromatograms), see peaks.

Methods currently implemented for mzR

fileName

signature(object = "mzR"): ...

Methods currently implemented for mzRramp

analyzer

signature(object = "mzRramp"): ...

close

signature(con = "mzRramp"): ...

detector

signature(object = "mzRramp"): ...

fileName

signature(object = "mzRramp"): ...

initializeRamp

signature(object = "mzRramp"): ...

instrumentInfo

signature(object = "mzRramp"): ...

ionisation

signature(object = "mzRramp"): ...

isInitialized

signature(object = "mzRramp"): ...

length

signature(x = "mzRramp"): ...

manufacturer

signature(object = "mzRramp"): ...

model

signature(object = "mzRramp"): ...

runInfo

signature(object = "mzRramp"): ...

Methods currently implemented for mzRpwiz

analyzer

signature(object = "mzRpwiz"): ...

detector

signature(object = "mzRpwiz"): ...

instrumentInfo

signature(object = "mzRpwiz"): ...

ionisation

signature(object = "mzRpwiz"): ...

length

signature(x = "mzRpwiz"): ...

manufacturer

signature(object = "mzRpwiz"): ...

model

signature(object = "mzRpwiz"): ...

runInfo

signature(object = "mzRpwiz"): ...

chromatogramsInfo

signature(object = "mzRpwiz"): ...

Methods currently implemented for mzRident

mzidInfo

signature(object = "mzRident"): ...

psms

signature(object = "mzRident"): ...

modifications

signature(object = "mzRident"): ...

substitutions

signature(object = "mzRident"): ...

database

signature(x = "mzRident"): ...

enzymes

signature(object = "mzRident"): ...

sourceInfo

signature(object = "mzRident"): ...

tolerance

signature(object = "mzRident"): ...

score

signature(object = "mzRident"): ...

para

signature(object = "mzRident"): ...

Author(s)

Steffen Neumann, Laurent Gatto, Qiang Kou

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")