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Read files from 'ChemStation' .D directories

Source: R/read_agilent_d.R
read_agilent_d.Rd

Agilent .ch files come in several different varieties. 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.

Usage

read_agilent_d(
  path,
  what = c("chroms", "dad", "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 .ch file

what

Whether to extract chromatograms (chroms), DAD data (dad) and/or peak tables peak_table. Accepts multiple arguments. ms_spectra. Accepts multiple arguments.

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.

metadata_format

Format to output metadata. Either chromconverter or raw.

collapse

Logical. Whether to collapse lists that only contain a single element.

Value

A list of chromatograms in the format specified by data_format and #' format_out. 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. Metadata can be attached to the chromatogram as attributes if read_metadata is TRUE.

Author

Ethan Bass