Read 'Agilent' DX files

Reads 'Agilent' .dx files.

Usage

read_agilent_dx(
  path,
  what = c("chroms", "dad"),
  path_out = NULL,
  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 .dx file.

what

Whether to extract chromatograms (chroms), DAD data (dad) and/or auxiliary instrumental data (instrument) (e.g., temperature, pressure, solvent composition, etc.). Accepts multiple arguments.

path_out

A directory to export unzipped files. If a path is not specified, the files will be written to a temp directory on the disk. The function will overwrite existing folders in the specified directory that share the basename of the file specified by path.

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 chromatogram in the format specified by format_out (retention time x wavelength).

Details

This function unzips 'Agilent' .dx into a temporary directory using unzip and calls the appropriate parser on the unzipped file.

See also

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

Author

Ethan Bass