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Read 'Agilent' DX files

Source: R/read_agilent_dx.R
read_agilent_dx.Rd

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), such as temperature, pressure or solvent composition. Accepts multiple arguments, and defaults to chroms and dad. When more than one is requested, any the archive does not contain are left out; a single one that is missing is an error.

path_out

A directory to export unzipped files. If a path is not specified, a temporary directory is used. The files are extracted into a folder named for path, overwriting any files of the same name already there.

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 (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 with one element per type in what, each a chromatogram or a list of chromatograms named by signal, in the format specified by format_out and data_format. With collapse = TRUE, a list of one element is replaced by that element.

Details

The archive is extracted to path_out, or to a temporary directory that is deleted afterwards, and its .ch, .uv and .it files are read with read_chemstation_ch, read_chemstation_uv and an internal reader for .it files.

Where the archive holds an injection.acmd file, the run_datetime and sample_injection_volume attributes are taken from it. Its run time records the offset from UTC, while the .ch and .uv headers give only the local time.

See also

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

Author

Ethan Bass

Examples

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