Create and check mzR objects from netCDF, mzXML, mzData or mzML files.

Description

The openMSfile constructor will create a new format-specifc mzR object, open 'filename' file and all header information is loaded as a Rcpp module and made accessible through the ramp or pwiz slot of the resulting object.

The openIDfile constructor will create a new format-specifc mzR object, open 'filename' file and all information is loaded as a Rcpp module. The mzid format is supported throught pwiz backend. Only mzIdentML 1.1 is supported.

Usage

 openMSfile(filename, backend=c("Ramp", "pwiz", "netCDF"), verbose = FALSE)

 initializeRamp(object)

 isInitialized(object)

 fileName(object, ...)
 
 openIDfile(filename, verbose = FALSE)

Arguments

Author(s)

Steffen Neumann, Laurent Gatto, Qiang Kou

Examples

 library(msdata)
 filepath <- system.file("microtofq", package = "msdata")
 file <- list.files(filepath, pattern="MM14.mzML",
                     full.names=TRUE, recursive = TRUE)
 mz <- openMSfile(file)
 fileName(mz)
 runInfo(mz)
 close(mz)

 ## Not run: 
    ## to use another backend
    mz <- openMSfile(file, backend = "pwiz")
    mz
  
## End(Not run)
  
  file <- system.file("mzid", "Tandem.mzid.gz", package="msdata")
  mzid <- openIDfile(file)
  softwareInfo(mzid)
  enzymes(mzid)

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)

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> library(mzR)
Loading required package: Rcpp
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mzR/openMSfile.Rd_%03d_medium.png", width=480, height=480)
> ### Name: openMSfile
> ### Title: Create and check mzR objects from netCDF, mzXML, mzData or mzML
> ###   files.
> ### Aliases: openMSfile initializeRamp isInitialized fileName openIDfile
> 
> ### ** Examples
> 
>  library(msdata)
>  filepath <- system.file("microtofq", package = "msdata")
>  file <- list.files(filepath, pattern="MM14.mzML",
+                      full.names=TRUE, recursive = TRUE)
>  mz <- openMSfile(file)
>  fileName(mz)
[1] "/home/ddbj/local/lib64/R/library/msdata/microtofq/MM14.mzML"
>  runInfo(mz)
$scanCount
[1] 112

$lowMz
[1] 0

$highMz
[1] 0

$dStartTime
[1] 270.334

$dEndTime
[1] 307.678

$msLevels
[1] 1

>  close(mz)
> 
>  ## Not run: 
> ##D     ## to use another backend
> ##D     mz <- openMSfile(file, backend = "pwiz")
> ##D     mz
> ##D   
> ## End(Not run)
>   
>   file <- system.file("mzid", "Tandem.mzid.gz", package="msdata")
>   mzid <- openIDfile(file)
>   softwareInfo(mzid)
[1] "xtandem x! tandem CYCLONE (2010.06.01.5) "   
[2] "ProteoWizard MzIdentML 3.0.6239 ProteoWizard"
>   enzymes(mzid)
     name nTermGain cTermGain minDistance missedCleavages
1 Trypsin         H        OH           0               1
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>