Read ThermoRaw files into R using ThermoRawFileParser — read

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

Usage

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

Arguments

path_in: Path to 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 .

Author

Ethan Bass

Examples

if (FALSE) {
read_thermoraw(path)
}