mzR-class: Class 'mzR' and sub-classes

In sneumann/mzR-playground: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)

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 is the only available implementation. It uses the ISB 'RAMP' random access C/C++ API 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.

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

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"): ...

get3Dmap

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

header

signature(object = "mzRramp", scans = "missing"): ...

header

signature(object = "mzRramp", scans = "numeric"): ...

header

signature(object = "mzRnetCDF", scans = "missing"): ...

header

signature(object = "mzRnetCDF", scans = "numeric"): ...

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"): ...

peaksCount

signature(object = "mzRramp", scans = "missing"): ...

peaksCount

signature(object = "mzRramp", scans = "numeric"): ...

peaks

signature(object = "mzRramp", scans = "missing"): ...

peaks

signature(object = "mzRramp", scans = "numeric"): ...

peaks

signature(object = "mzRnetCDF", scans = "missing"): ...

peaks

signature(object = "mzRnetCDF", scans = "numeric"): ...

runInfo

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

Author(s)

Steffen Neumann and Laurent Gatto

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)

sneumann/mzR-playground documentation built on May 30, 2019, 6 a.m.