Read ThermoRaw

Converts a 'Thermo' .raw file to mzML with the ThermoRawFileParser and reads the result with read_mzml.

Usage

read_thermoraw(
  path,
  path_out = NULL,
  format_out = c("matrix", "data.frame", "data.table"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  centroid = TRUE,
  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 temporary directory is used and deleted afterwards.

format_out

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

read_metadata

Logical. Whether to attach metadata. Defaults to TRUE.

metadata_format

Format to output metadata. Either chromconverter (standardized field names) or raw (vendor field names, unmapped).

centroid

Logical. Whether to centroid profile spectra with the vendor's peak picking. Defaults to TRUE. Set it to FALSE to keep profile spectra as acquired, which are about ten times larger. Spectra acquired in centroid mode stay centroided either way.

verbose

Logical. Whether to print output from ThermoRawFileParser to the console. Ignored on Windows, where the output is always printed.

Value

A list of chromatograms, as returned by read_mzml, in the format specified by format_out.

Details

The ThermoRawFileParser must be installed separately.

Side effects

If path_out is specified, the mzML file (and, if read_metadata is TRUE, a metadata .txt file) is left there.

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)
} # }