metadata {mzR} | R Documentation

## 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`, `dEndTime` and `startTimeStamp`. Note that `startTimeStamp` can only be extracted from mzML files using the pwiz backend or from CDF files. A `NA` is reported if its value is not available. 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)
    specParams(object)

### Arguments

`object` | An instantiated `mzR` object.
`x` | An instantiated `mzR` object.
`...` | Additional arguments, currently ignored.

### 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)

     file <- system.file("microtofq/MM8.mzML", package = "msdata")
     mz <- openMSfile(file)
     fileName(mz)
     instrumentInfo(mz)
     runInfo(mz)
     close(mz)

     file <- system.file("cdf/ko15.CDF", package = "msdata")
     mz <- openMSfile(file, backend = "netCDF")
     fileName(mz)
     instrumentInfo(mz)
     runInfo(mz)
     close(mz)

     file <- system.file("mzid", "Tandem.mzid.gz", package="msdata")
     mzid <- openIDfile(file)
     softwareInfo(mzid)
     enzymes(mzid)

[Package mzR version 2.16.2 Index]