Read ThermoRaw

Converts ThermoRawFiles to mzML by calling the ThermoRawFileParser from the command-line.

Usage

read_thermoraw(
  path,
  path_out = NULL,
  format_out = c("matrix", "data.frame"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  verbose = getOption("verbose")
)

Arguments

path

Path to 'Thermo' .raw file.

path_out

Path to directory to export mzML files. If path_out isn't specified, a temp directory will be used.

format_out

R format. Either matrix or data.frame.

read_metadata

Whether to read metadata from file.

metadata_format

Format to output metadata. Either chromconverter or raw.

verbose

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

Value

A chromatogram in the format specified by format_out.

Details

To use this function, the ThermoRawFileParser must be manually installed.

Side effects

Exports chromatograms in mzML format to the folder specified by path_out.

References

Hulstaert Niels, Jim Shofstahl, Timo Sachsenberg, Mathias Walzer, Harald Barsnes, Lennart Martens, and Yasset Perez-Riverol. ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion. Journal of Proteome Research 19, no. 1 (January 3, 2020): 537–42. doi:10.1021/acs.jproteome.9b00328 .

See also

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

Author

Ethan Bass

Examples

if (FALSE) { # \dontrun{
read_thermoraw(path)
} # }