read_thermoraw: Read ThermoRaw files into R using ThermoRawFileParser

In ethanbass/chromConverter: Chromatographic File Converter

Read ThermoRaw files into R using ThermoRawFileParser

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")
)

Arguments

path	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.

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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1021/acs.jproteome.9b00328")}.

Examples

## Not run: 
read_thermoraw(path)

## End(Not run)

ethanbass/chromConverter documentation built on Jan. 14, 2025, 2:11 a.m.