mzR-class {mzR} | R Documentation

## 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. `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.

### 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 an `mzR` object, one can write it into a new 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")`: ...

specParams

  `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")

[Package mzR version 2.21.1 Index]