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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), auxiliary instrumental data (instrument), such as temperature, pressure or solvent composition, and/or mass spectra (MS1) with the total ion chromatogram (TIC) and base peak chromatogram (BPC). 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. Mass spectra and the BPC are always in long format, with rt, mz and intensity columns, and are returned as a data.table when format_out is matrix. 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.

The mass spectra of an MS injection are not in the archive. They are in the .MSScan.bin and .MSPeak.bin files of the same name beside it. The first is needed for MS1, TIC and BPC, the second for MS1. MSScan.bin holds one record per scan, laid out as the archive's MSData/MSScan.xsd describes, which gives the retention time, TIC and base peak of the scan and the location of its spectrum in MSPeak.bin. Each spectrum there is the scan's m/z values followed by as many intensities, as 32- or 64-bit floats or 32-bit integers depending on the scan's spectrum format and size. Only scans at MS level 1 are read into MS1, while the TIC and BPC cover every scan.

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)
} # }