read_chemstation_ms {chromConverter} | R Documentation |
Read 'Agilent ChemStation' MS file.
Description
Reads 'Agilent ChemStation MSD Spectral Files' beginning with
x01/x32/x00/x00
.
Usage
read_chemstation_ms(
path,
what = c("MS1", "BPC", "TIC"),
format_out = c("matrix", "data.frame", "data.table"),
data_format = c("wide", "long"),
read_metadata = TRUE,
metadata_format = c("chromconverter", "raw"),
collapse = TRUE
)
Arguments
path |
Path to 'Agilent' |
what |
What stream to get: current options are |
format_out |
Class of output. Either |
data_format |
Whether to return data in |
read_metadata |
Logical. Whether to attach metadata. Defaults to |
metadata_format |
Format to output metadata. Either |
collapse |
Logical. Whether to collapse lists that only contain a single
element. Defaults to |
Value
A 2D chromatogram in the format specified by data_format
and
format_out
. If data_format
is wide
, the chromatogram will
be returned with retention times as rows and a single column for the intensity.
If long
format is requested, two columns will be returned: one for the
retention time and one for the intensity. The format_out
argument
determines whether the chromatogram is returned as a matrix
,
data.frame
, or data.table
. Metadata can be attached to the
chromatogram as attributes
if read_metadata
is TRUE
.
Note
Many thanks to Evan Shi and Eugene Kwan for providing helpful information on the structure of these files in the rainbow documentation.
Author(s)
Ethan Bass
See Also
Other 'Agilent' parsers:
read_agilent_d()
,
read_agilent_dx()
,
read_chemstation_ch()
,
read_chemstation_csv()
,
read_chemstation_reports()
,
read_chemstation_uv()
Examples
## Not run:
read_chemstation_ms(path)
## End(Not run)