Skip to contents

Read 'Agilent ChemStation' MS file.

Source: R/read_chemstation_ms.R
read_chemstation_ms.Rd

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 = "long",
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  collapse = TRUE
)

Arguments

path

Path to 'Agilent' .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 (default) 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 list of chromatograms in the format specified by data_format and format_out. If data_format is wide, 2D chromatograms will be returned with retention times as rows and a single column for the intensity. Otherwise, two columns will be returned: one for the retention time and one for the intensity. MS data will always be returned in long format. 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.

See also

Other 'Agilent' parsers: read_agilent_d(), read_agilent_dx(), read_chemstation_ch(), read_chemstation_csv(), read_chemstation_reports(), read_chemstation_uv()

Author

Ethan Bass

Examples

if (FALSE) { # \dontrun{
read_chemstation_ms(path)
} # }