mzR-class {mzR} | R Documentation |
mzR
and sub-classesThe 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.
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.
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.
Class "Versioned"
, directly.
For methods to access raw data (spectra and chromatograms), see
peaks
.
Methods currently implemented for mzR
signature(object = "mzR")
: ...
Methods currently implemented for mzRramp
signature(object = "mzRramp")
: ...
signature(con = "mzRramp")
: ...
signature(object = "mzRramp")
: ...
signature(object = "mzRramp")
: ...
signature(object = "mzRramp")
: ...
signature(object = "mzRramp")
: ...
signature(object = "mzRramp")
: ...
signature(object = "mzRramp")
: ...
signature(x = "mzRramp")
: ...
signature(object = "mzRramp")
: ...
signature(object = "mzRramp")
: ...
signature(object = "mzRramp")
: ...
Methods currently implemented for mzRpwiz
signature(object = "mzRpwiz")
: ...
signature(object = "mzRpwiz")
: ...
signature(object = "mzRpwiz")
: ...
signature(object = "mzRpwiz")
: ...
signature(x = "mzRpwiz")
: ...
signature(object = "mzRpwiz")
: ...
signature(object = "mzRpwiz")
: ...
signature(object = "mzRpwiz")
: ...
signature(object = "mzRpwiz")
: ...
Methods currently implemented for mzRident
signature(object = "mzRident")
: ...
signature(object = "mzRident")
: ...
signature(object = "mzRident")
: ...
signature(object = "mzRident")
: ...
signature(x = "mzRident")
: ...
signature(object = "mzRident")
: ...
signature(object = "mzRident")
: ...
signature(object = "mzRident")
: ...
signature(object = "mzRident")
: ...
signature(object = "mzRident")
: ...
signature(object = "mzRident")
: ...
Steffen Neumann, Laurent Gatto, Qiang Kou
RAMP: http://tools.proteomecenter.org/wiki/index.php?title=Software:RAMP Proteowizard: http://proteowizard.sourceforge.net/
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")