Access the metadata from an mzR object.

Description

Accessors to the analytical setup metadata of a run. runInfo will show a summary of the experiment as a named list, including scanCount, lowMZ, highMZ, dStartTime and dEndTime. The instrumentInfo method returns a named list including instrument manufacturer, model, ionisation technique, analyzer and detector. mzRpwiz will give more additional information including information on sample, software using and original source file. These individual pieces of information can also be directly accessed by the specific methods. mzidInfo is used for the mzR object created from a mzid file. It returns basic information on this mzid file including file provider, creation date, software, database, enzymes and spectra data format. The mzidInfo will return the scoring results in identification. It will return different results for different searching software used.

Usage

runInfo(object)
chromatogramsInfo(object)
analyzer(object)
detector(object)
instrumentInfo(object)
ionisation(object)
softwareInfo(object)
sampleInfo(object)
sourceInfo(object)
model(object)
mzidInfo(object)
modifications(object, ...)
psms(object, ...)
substitutions(object)
database(object, ...)
enzymes(object)
tolerance(object)
score(x, ...)
para(object)

Arguments

Author(s)

Steffen Neumann, Laurent Gatto and Qiang Kou

See Also

See for example peaks to access the data for the spectra in a "mzR" class.

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)
 instrumentInfo(mz)
 close(mz)
 
 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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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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/metadata.Rd_%03d_medium.png", width=480, height=480)
> ### Name: metadata
> ### Title: Access the metadata from an 'mzR' object.
> ### Aliases: analyzer detector instrumentInfo ionisation manufacturer model
> ###   runInfo chromatogramsInfo softwareInfo sampleInfo sourceInfo mzidInfo
> ###   modifications psms substitutions database enzymes tolerance score
> ###   para
> 
> ### ** 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"
>  instrumentInfo(mz)
$manufacturer
[1] "Unknown"

$model
[1] "instrument model"

$ionisation
[1] "electrospray ionization"

$analyzer
[1] "mass analyzer type"

$detector
[1] "detector type"

>  close(mz)
>  
>  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 
>