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Read 'Agilent ChemStation' MS file.

Source: R/read_chemstation_ms.R
read_chemstation_ms.Rd

Parser to read 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.

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

Ethan Bass