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Read 'Agilent ChemStation' CH files

Source: R/read_chemstation_ch.R
read_chemstation_ch.Rd

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,
  source_file = NULL
)

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 (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 multiply the data by the file's scaling factor and add its intercept. Defaults to TRUE. 'MassHunter' seems to ignore the scaling factor in at least some types of 'ChemStation' files.

source_file

Source file from which chromatogram data was originally derived.

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 row names 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 are attached to the chromatogram as attributes if read_metadata is TRUE.

Details

'Agilent' .ch files come in several formats. This parser detects the version from the file and reads versions 8, 30, 130, 81, 179 and 181 from 'Agilent ChemStation' and 'Agilent OpenLab'; any other version is an error. Versions 30 and 130 are generally produced by ultraviolet detectors, and 81, 179 and 181 by flame ionization detectors (FID).

Note

This function was adapted from the Chromatography Toolbox (© James Dillon 2014).

See also

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

Author

Ethan Bass

Examples

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