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Parse files with OpenChrom

Source: R/call_openchrom.R
call_openchrom.Rd

Converts files with the OpenChrom command-line interface, then reads the converted files back into R. OpenChrom removed the command-line interface in version 1.5.0, and Lablicate no longer distributes older versions, so this function works only with an existing installation of OpenChrom 1.4 or earlier. It is deprecated for that reason.

Usage

call_openchrom(
  files,
  path_out = NULL,
  format_in,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  export_format = c("mzml", "csv", "cdf", "animl"),
  return_paths = FALSE,
  verbose = getOption("verbose")
)

Arguments

files

Path to files.

path_out

Directory to export converted files. Defaults to NULL, in which case the files go to a temporary directory that is deleted when the function returns.

format_in

Either msd for mass spectrometry data, csd for FID, ECD or NPD data, or wsd for DAD/UV data.

format_out

Class of output. Either matrix, data.frame, or data.table.

data_format

Whether to return data in wide (default) or long format.

export_format

Either mzml, csv, cdf, or animl. Defaults to mzml. mzml and cdf are available only for msd. OpenChrom versions before 1.4 can export only msd files, and only to csv, cdf or animl.

return_paths

Logical. If TRUE, the function will return a character vector of paths to the newly created files.

verbose

Logical. Whether to print output from OpenChrom to the console.

Value

If return_paths is FALSE, a list with one chromatogram per file, read back with read_mzml, read_cdf or read.csv according to export_format. format_out and data_format apply only to cdf files, except that format_out = "matrix" also converts csv files. animl files cannot be read back, so use return_paths = TRUE for them. If return_paths is TRUE, a character vector of paths to the newly created files.

Details

The call_openchrom function works by creating an xml batchfile and feeding it to the OpenChrom command-line interface. OpenChrom batchfiles consist of InputEntries (specifying the files you want to convert) and ProcessEntries (specifying what you want to do to the files). The parsers are organized into broad categories by detector-type and output format. The detector-types are msd (mass selective detectors), csd (current selective detectors, e.g., FID, ECD, NPD), and wsd (wavelength selective detectors, e.g., DAD, and UV/VIS). Thus, when calling the OpenChrom parsers, one of these three options must be specified using the format_in argument.

Note

Activating the OpenChrom command-line deactivates the graphical user interface (GUI). To keep using the GUI, install a second copy of OpenChrom and call that one from R.

Side effects

Chromatograms are exported in the format specified by export_format to the folder specified by path_out.

References

Wenig, Philip and Odermatt, Juergen. OpenChrom: A Cross-Platform Open Source Software for the Mass Spectrometric Analysis of Chromatographic Data. BMC Bioinformatics 11, no. 1 (July 30, 2010): 405. doi:10.1186/1471-2105-11-405 .

See also

Other external parsers: call_entab(), call_rainbow(), read_thermoraw(), sp_converter(), uv_converter()

Author

Ethan Bass

Examples

if (FALSE) { # \dontrun{
call_openchrom("path/to/file.RAW", format_in = "msd", export_format = "mzml")
} # }