The writeMSData,MSnExp and writeMSData,OnDiskMSnExp saves
the content of a MSnExp or OnDiskMSnExp object to MS file(s) in
either mzML or mzXML format.
# S4 method for MSnExp,character
writeMSData(
object,
file,
outformat = c("mzml", "mzxml"),
merge = FALSE,
verbose = isMSnbaseVerbose(),
copy = FALSE,
software_processing = NULL
)OnDiskMSnExp or MSnExp object.
character with the file name(s). Its length has to match the
number of samples/files of x.
character(1) defining the format of the output files.
Default output format is "mzml".
logical(1) whether the data should be saved into a single
mzML file. Default is merge = FALSE, i.e. each sample is saved to
a separate file. Note: merge = TRUE is not yet implemented.
logical(1) if progress messages should be displayed.
logical(1) if metadata (data processings, original file names
etc) should be copied from the original files. See details for more
information.
optionally provide specific data processing steps.
See documentation of the software_processing parameter of
mzR::writeMSData().
The writeMSData method uses the proteowizard libraries through
the mzR package to save the MS data. The data can be written to
mzML or mzXML files with or without copying additional metadata
information from the original files from which the data was read by the
readMSData() function. This can be set using the copy parameter.
Note that copy = TRUE requires the original files to be available and
is not supported for input files in other than mzML or mzXML format.
All metadata related to the run is copied, such as instrument
information, data processings etc. If copy = FALSE only processing
information performed in R (using MSnbase) are saved to the mzML file.
Currently only spectrum data is supported, i.e. if the original mzML file contains also chromatogram data it is not copied/saved to the new mzML file.
General spectrum data such as total ion current, peak count, base peak m/z or base peak intensity are calculated from the actual spectrum data before writing the data to the files.
For MSn data, if the OnDiskMSnExp or MSnExp does not contain also
the precursor scan of a MS level > 1 spectrum (e.g. due to filtering on
the MS level) precursorScanNum is set to 0 in the output file to
avoid potentially linking to a wrong spectrum.
The exported mzML file should be valid according to the mzML 1.1.2
standard. For exported mzXML files it can not be guaranteed that they
are valid and can be opened with other software than mzR/MSnbase.