read_thermoraw {chromConverter} | R Documentation |
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")
)
Arguments
path |
Path to 'Thermo' |
path_out |
Path to directory to export |
format_out |
R format. Either |
read_metadata |
Whether to read metadata from file. |
metadata_format |
Format to output metadata. Either |
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. doi:10.1021/acs.jproteome.9b00328.
See Also
Other external parsers:
call_entab()
,
call_openchrom()
,
call_rainbow()
,
sp_converter()
,
uv_converter()
Examples
## Not run:
read_thermoraw(path)
## End(Not run)