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. You can also open mz5 file by using mzRpwiz.

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

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"): ...

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")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(mzR)
Loading required package: Rcpp
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mzR/mzR-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mzR-class
> ### Title: Class 'mzR' and sub-classes
> ### Aliases: mzR-class mzRramp-class mzRnetCDF-class mzRpwiz-class
> ###   mzRident-class class:mzR class:mzRramp class:mzRnetCDF class:mzRpwiz
> ###   class:mzRident close,mzRpwiz-method close,mzRramp-method
> ###   close,mzRnetCDF-method close analyzer,mzRramp-method
> ###   analyzer,mzRpwiz-method analyzer,mzRnetCDF-method
> ###   detector,mzRramp-method detector,mzRpwiz-method
> ###   detector,mzRnetCDF-method fileName,mzR-method get3Dmap,mzRramp-method
> ###   get3Dmap,mzRpwiz-method header,mzRramp,missing-method
> ###   header,mzRramp,numeric-method header,mzRpwiz,missing-method
> ###   header,mzRpwiz,numeric-method header,mzRnetCDF,missing-method
> ###   header,mzRnetCDF,numeric-method initializeRamp,mzRramp-method
> ###   instrumentInfo,mzRramp-method instrumentInfo,mzRpwiz-method
> ###   instrumentInfo,mzRnetCDF-method ionisation,mzRramp-method
> ###   ionisation,mzRpwiz-method ionisation,mzRnetCDF-method
> ###   isInitialized,mzRramp-method isInitialized,mzRnetCDF-method
> ###   length,mzRident-method length,mzRramp-method length,mzRpwiz-method
> ###   length,mzRnetCDF-method length manufacturer,mzRramp-method
> ###   manufacturer,mzRpwiz-method manufacturer,mzRnetCDF-method
> ###   model,mzRramp-method model,mzRpwiz-method model,mzRnetCDF-method
> ###   peaksCount,mzRramp,missing-method peaksCount,mzRramp,numeric-method
> ###   peaksCount,mzRpwiz,missing-method peaksCount,mzRpwiz,numeric-method
> ###   peaks,mzRramp-method peaks,mzRramp-method peaks,mzRpwiz-method
> ###   peaks,mzRpwiz-method peaks,mzRnetCDF-method peaks,mzRnetCDF-method
> ###   runInfo,mzRramp-method runInfo,mzRpwiz-method
> ###   runInfo,mzRnetCDF-method chromatogramsInfo,mzRpwiz-method
> ###   softwareInfo,mzRpwiz-method softwareInfo,mzRident-method
> ###   sampleInfo,mzRpwiz-method sourceInfo,mzRpwiz-method
> ###   mzidInfo,mzRident-method psms,mzRident-method
> ###   modifications,mzRident-method substitutions,mzRident-method
> ###   database,mzRident-method enzymes,mzRident-method
> ###   sourceInfo,mzRident-method tolerance,mzRident-method
> ###   score,mzRident-method para,mzRident-method
> ### Keywords: classes
> 
> ### ** 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")
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>