chromConverter (version 0.7.5)

read_thermoraw: Read ThermoRaw

Description

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")
)

Value

A chromatogram in the format specified by format_out.

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.

Side effects

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

Author

Ethan Bass

Details

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

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. tools:::Rd_expr_doi("10.1021/acs.jproteome.9b00328").

See Also

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

Examples

if (FALSE) {
read_thermoraw(path)
}