Read 'Agilent ChemStation' MS files

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

Which streams to return: MS1, BPC and/or TIC. Defaults to all three.

format_out

Class of output. Either matrix, data.frame, or data.table.

data_format

Whether to return the BPC and TIC in long (default) or wide format. Mass spectra are always returned in long format.

read_metadata

Logical. Whether to attach metadata. Defaults to TRUE.

metadata_format

Format to output metadata. Either chromconverter (standardized field names) or raw (vendor field names, unmapped).

collapse

Logical. Whether to collapse lists that only contain a single element. Defaults to TRUE.

Value

A list of the streams in what, in the format specified by format_out. In wide format, the BPC and TIC have retention times as rows and a single intensity column; in long format, a retention time column and an intensity column. 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 are attached as attributes if read_metadata is TRUE. With collapse = TRUE, a list of one stream is replaced by that stream.

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_agilent_rslt(), read_chemstation_ch(), read_chemstation_csv(), read_chemstation_logs(), read_chemstation_reports(), read_chemstation_uv()

Author

Ethan Bass

Examples

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