read_thermoraw {chromConverter}

Read ThermoRaw files into R using ThermoRawFileParser

Description

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

Usage

read_thermoraw(
  path_in,
  path_out,
  format_out = c("matrix", "data.frame"),
  read_metadata = TRUE
)

Arguments

path_in

path to file

path_out

directory to export mzML files.

format_out

R format. Either matrix or data.frame.

read_metadata

Whether to read metadata from file.

Details

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

Value

A chromatogram in the format specified by format_out.

Side effects

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

Author(s)

Ethan Bass

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.

Examples

## Not run: 
read_thermoraw(path)

## End(Not run)