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Read 'Agilent ChemStation' DAD files

Source: R/read_chemstation_uv.R
read_chemstation_uv.Rd

Agilent .uv files come in several formats. This parser detects the version from the file and reads versions 31 and 131 from 'Agilent ChemStation' and 'Agilent OpenLab'; any other version is an error.

Usage

read_chemstation_uv(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  scale = TRUE,
  source_file = NULL
)

Arguments

path

Path to 'Agilent' .uv file.

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).

scale

Whether to scale the data by the scaling factor present in the file. Defaults to TRUE.

source_file

Source file from which UV data was originally derived.

Value

A 3D chromatogram in the format specified by data_format and format_out. If data_format is wide, the chromatogram will be returned with retention times as row names and wavelengths as columns. If long format is requested, three columns will be returned: one for the retention time, one for the wavelength and one for the intensity. The format_out argument determines whether the chromatogram is returned as a matrix, data.frame, or data.table. Metadata are attached to the chromatogram as attributes if read_metadata is TRUE.

Details

Retention times are read from each spectrum, so they are unevenly spaced when the detector did not store every spectrum. Interpolate onto a common time axis before comparing runs.

Note

This function was adapted from the parser in the rainbow project licensed under GPL 3 by Evan Shi https://rainbow-api.readthedocs.io/en/latest/agilent/uv.html.

See also

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

Author

Ethan Bass

Examples

if (FALSE) { # interactive()
read_chemstation_uv("tests/testthat/testdata/dad1.uv")
}