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Read files from 'Agilent ChemStation' .D directories

Source: R/read_agilent_d.R
read_agilent_d.Rd

Reads the .ch, .uv, Report.TXT (or Result.xml) and LCDIAG.REG files in an 'Agilent' .D directory. Other files in the directory are ignored.

Usage

read_agilent_d(
  path,
  what = c("dad", "chroms", "peak_table", "MS1", "MS2", "TIC", "BPC"),
  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' .D directory.

what

Whether to extract chromatograms (chroms), DAD data (dad), peak tables (peak_table) and/or instrument traces (instrument), such as pump pressure, flow, solvent composition and temperature, read from LCDIAG.REG, and/or mass spectra (MS1, MS2) with the total ion chromatogram (TIC) and base peak chromatogram (BPC). Accepts multiple arguments, and defaults to all of these but instrument. Types the directory does not contain are left out, and it is an error if it contains none of them. With the default, mass spectrometry data that cannot be read are also left out, with a warning, if the directory holds other data. The TIC and BPC are read from the scan records, so they are returned even when the spectra cannot be.

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 found, each a chromatogram or a list of them named by file, in the format specified by format_out and data_format. If data_format is wide, the chromatograms will be returned with retention times as rows and columns containing signal intensity for each signal. If long format is requested, retention times will be in the first column. The format_out argument determines whether the chromatogram is returned as a matrix, data.frame or data.table. Peak tables are returned in the chromatographr layout described in read_peaklist, named by wavelength (e.g. "254"), and keep the report's name for the signal as signal_descriptor. They are read from Result.xml where the directory has one, since unlike Report.TXT it records where each peak starts and ends. Mass spectra and the BPC are always in long format, with rt, mz and intensity columns, and a precursor_mz column before mz for MS2. They are returned as a data.table when format_out is matrix. Each table of spectra has a scan_info attribute with one row per scan, giving its scan, rt, ms_level, polarity and scan_type ("scan", "SIM", "MRM" or "product ion scan", and NA for any other type), and for MS2 its precursor_mz and collision_energy. Metadata are attached as attributes if read_metadata is TRUE. With collapse = TRUE, a list of one element is replaced by that element.

Details

Instrument traces are named from LCDIAG.REG, so the names differ between 'ChemStation' revisions and/or instruments (e.g. "PMP1, Pressure" and "PMP1, PMP1A, Pressure"). Parts of the file that cannot be read are skipped with a warning.

Mass spectra are read from the AcqData folder of a 'MassHunter' .d directory. Its MSScan.bin and MSScan.xsd describe every scan, as in read_agilent_dx, and the spectra are in MSPeak.bin, or in MSProfile.bin for profiles. Each profile starts with its first m/z and the step between points, as two doubles or two 32-bit floats, followed by the intensities as 32-bit floats or integers respectively. The points are spaced by the scan's SamplingPeriod rather than the stored step, which can be slightly smaller. Spectra can be read only from unit-resolution instruments, such as single quadrupole GC-MS and LC-MS, and triple quadrupole LC-MS. MS1 holds the scans at MS level 1 and MS2 the product ion and MRM scans, each with the m/z it selected in the first quadrupole as precursor_mz. Neutral loss and precursor ion scans are skipped with a warning. The TIC and BPC come from the record of every scan, so they are also returned for runs whose spectra cannot be read. For high-resolution spectra, try parser = "rainbow" with centroid or hrms.

See also

Other 'Agilent' parsers: read_agilent_dx(), 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

path <- system.file("extdata", "benzoxazinoid_standards", "BENZOS_250PPM.D",
                    package = "chromConverter")
run <- read_agilent_d(path)
names(run$chroms)
#> [1] "dad1A" "dad1B" "dad1C" "dad1D" "dad1E"
pump <- read_agilent_d(path, what = "instrument")
names(pump)
#> [1] "PMP1, Pressure"  "PMP1, Flow"      "PMP1, Solvent A" "PMP1, Solvent B"
#> [5] "PMP1, Solvent C" "PMP1, Solvent D"