read_chemstation_ms: Read 'Agilent ChemStation' MS file.

In ethanbass/chromConverter: Chromatographic File Converter

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 .ms file
what	What stream to get: current options are MS1, BPC and/or TIC. If a stream is not specified, the function will return all streams.
format_out	Class of output. Either matrix, data.frame, or data.table.
data_format	Whether to return data in wide or long format.
read_metadata	Logical. Whether to attach metadata. Defaults to TRUE.
metadata_format	Format to output metadata. Either chromconverter or raw.
collapse	Logical. Whether to collapse lists that only contain a single element. Defaults to TRUE.

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)

ethanbass/chromConverter documentation built on March 29, 2025, 5:22 a.m.