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Write ANDI MS CDF file from chromatogram

Source: R/write_andi_ms.R
write_andi_ms.Rd

Exports mass spectrometry data in ANDI (Analytical Data Interchange) MS format (ASTM E1947-98). A total ion chromatogram is derived from the MS1 scans if the supplied object does not already carry one.

Usage

write_andi_ms(
  x,
  path_out,
  sample_name = NULL,
  force = FALSE,
  ms_params = list()
)

Arguments

x

A list of chromatograms containing an element whose name includes MS (e.g. MS1), or a single chromatogram of MS1 scans, in wide or long format.

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_name attribute.

force

Whether to overwrite existing files at the specified path. Defaults to FALSE.

ms_params

A list of settings recorded in the file: ionization_mode, ionization_polarity, detector_type, scan_function and experiment_type. A setting that is not given is taken from the chromatogram's metadata where it records one: the polarity from its polarity attribute, the scan function from scan_type, and the ionization mode and detector type from its ms_params attribute. Failing that, the defaults are "Electron Impact", "Positive Polarity" and "Electron Multiplier", and a scan function is left out of the file. experiment_type is not read from metadata and defaults to "Centroided Mass Spectrum".

Value

Invisibly returns the path to the written CDF file.

Details

Retention times are written in seconds, the only time unit the specification suggests, and declared in raw_data_time_units. A chromatogram is converted unless its time_unit already reports seconds, so one whose unit is missing or unrecognized is taken to be in minutes.

Side effects

Exports mass spectrometry data in ANDI MS format (netCDF) in the directory specified by path_out. The file will be named according to the value of sample_name. If no sample_name is provided, the sample_name attribute will be used if it exists.

See also

Other write functions: write_andi_chrom(), write_chroms(), write_mzml()

Author

Ethan Bass

Examples

if (FALSE) { # \dontrun{
write_andi_ms(chrom, path_out = "path/to/directory")
} # }