Description Objects from the Class Slots Extends Methods Author(s) References Examples
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. mzRident
is used as an
interface to mzIdentML
files.
IMPORTANT: New developers that need to access and manipulate raw mass
spectrometry data are advised against using this infrastucture
directly. They are invited to use the corresponding MSnExp
(with on disk mode) from the MSnbase package instead. The
latter supports reading multiple files at once and offers access to
the spectra data (m/z and intensity) as well as all the spectra
metadata using a coherent interface. The MSnbase infrastructure itself
used the low level classes in mzR, thus offering fast and efficient
access.
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 an mzR
object, one can write it into a new 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/
1 2 3 4 5 6 7 8 9 | 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")
|
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