This function constructs mzML files using a streaming XML-writing approach, generating and writing XML content directly to a file connection. This method is memory-efficient and fast, making it well-suited for large mzML files. However, it may be less flexible than DOM-based methods for handling complex XML structures or large-scale modifications after writing has begun.
Usage
write_mzml(
data,
path_out,
sample_name = NULL,
what = NULL,
instrument_info = NULL,
compress = TRUE,
indexed = TRUE,
force = FALSE,
show_progress = TRUE,
verbose = getOption("verbose")
)Arguments
- data
List of data.frames or data.tables containing spectral data.
- path_out
The path to write the file.
- sample_name
The name of the file. If a name is not provided, the name will be derived from the
sample_nameattribute.- what
Which streams to write to mzML:
"ms1","ms2","tic","bpc", and/or"dad".- instrument_info
Instrument info to write to mzML file.
- compress
Logical. Whether to use zlib compression. Defaults to
TRUE.- indexed
Logical. Whether to write indexed mzML. Defaults to
TRUE.- force
Logical. Whether to overwrite existing files at
path_out. Defaults toFALSE.- show_progress
Logical. Whether to show progress bar. Defaults to
TRUE.- verbose
Logical. Whether or not to print status messages.
Details
This function constructs mzML files by writing XML strings directly to a file connection. While this approach is memory-efficient and fast, it may be less flexible for handling complex XML structures.
The function supports writing various types of spectral data including MS1, MS2, TIC (Total Ion Current), BPC (Base Peak Chromatogram), and DAD (Diode Array Detector) data.
If indexed = TRUE, the function will create an indexed mzML file, which allows faster random access to spectra.