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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"),
  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. Accepts multiple arguments, and defaults to dad, chroms and peak_table. Types the directory does not contain are left out, and it is an error if it contains none of them.

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. 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.

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"