Read 'Agilent ChemStation' CH files

Reads 'Agilent ChemStation' .ch files.

Usage

read_chemstation_ch(
  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' .ch file.
format_out: Class of output. Either matrix, data.frame, or data.table.
data_format: Whether to return data in wide or long format.
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. 'MassHunter' seems to ignore the scaling factor in at least some types of 'ChemStation' files.

Value

A 2D 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 a single column for the intensity. If long format is requested, two columns will be returned: one for the retention time and one for the intensity. The format_out argument determines whether the chromatogram is returned as a matrix, data.frame, or data.table. Metadata can be attached to the chromatogram as attributes if read_metadata is TRUE.

Details

'Agilent' .ch 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 30 and 130, which are generally produced by ultraviolet detectors, as well as 81, 179, and 181 which are generally produced by flame ionization (FID) detectors.

Note

Author

Ethan Bass

Examples

if (FALSE) { # interactive()
read_chemstation_ch("tests/testthat/testdata/chemstation_130.ch")
}