writeMSData,MSnExp,character-method {MSnbase} | R Documentation |
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 signature 'MSnExp,character' writeMSData(object, file, outformat = c("mzml", "mzxml"), merge = FALSE, verbose = isMSnbaseVerbose(), copy = FALSE, software_processing = NULL)
object |
|
file |
|
outformat |
|
merge |
|
verbose |
|
copy |
|
software_processing |
optionally provide specific data processing steps.
See documentation of the |
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.
Johannes Rainer