Read 'Agilent ChemStation' DAD files

Agilent .uv files come in several different formats. This parser can automatically detect and read several versions of these files from 'Agilent ChemStation' and 'Agilent OpenLab', including versions 31 and 131.

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
)

Arguments

path: Path to 'Agilent' .uv file.
format_out: Class of output. Either matrix, data.frame, or data.table.
data_format: Either wide (default) or long.
read_metadata: Logical. Whether to attach metadata. Defaults to TRUE.
metadata_format: Format to output metadata. Either chromconverter or raw.
scale: Whether to scale the data by the scaling factor present in the file. Defaults to TRUE.

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 rows 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 or data.frame. Metadata can be attached to the chromatogram as attributes if read_metadata is TRUE.

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.

Author

Ethan Bass

Examples

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