writeMSData,XCMSnExp,character-method {xcms} | R Documentation

## Export MS data to mzML/mzXML files

### Description

`writeMSData` exports mass spectrometry data in mzML or mzXML format. If adjusted retention times are present, these are used as retention time of the exported spectra.

### Usage

    ## S4 method for signature 'XCMSnExp,character'
    writeMSData(
      object,
      file,
      outformat = c("mzml", "mzxml"),
      copy = FALSE,
      software_processing = NULL,
      ...
    )

### Arguments

`object` | XCMSnExp object with the mass spectrometry data.
`file` | `character` with the file name(s). The length of this parameter has to match the number of files/samples of `object`.
`outformat` | `character(1)` defining the format of the output files ( either `"mzml"` or `"mzxml"`).
`copy` | `logical(1)` if metadata (data processing, software used, original file names etc) should be copied from the original files.
`software_processing` | optionally provide specific data processing steps. See documentation of the `software_processing` parameter of `mzR::writeMSData()`.
`...` | Additional parameters to pass down to the `writeMSData()` function in the `MSnbase` package, such as `outformat` to specify the output format (`"mzml"` or `"mzxml"`) or `copy` to specify whether general information from the original MS data files (such as data processing, software etc) should be copied to the new files.

### Author(s)

Johannes Rainer

### See Also

`writeMSData()` function in the `MSnbase` package.

[Package xcms version 3.16.1 Index]