read_agilent_d: Read files from 'Agilent ChemStation' .D directories

In ethanbass/chromConverter: Chromatographic File Converter

Read files from 'Agilent ChemStation' .D directories

Description

Reads files from 'Agilent' .D directories.

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(s)

Ethan Bass

See Also

Other 'Agilent' parsers: read_agilent_dx(), read_chemstation_ch(), read_chemstation_csv(), read_chemstation_ms(), read_chemstation_reports(), read_chemstation_uv()

Examples

read_agilent_d("tests/testthat/testdata/RUTIN2.D")

ethanbass/chromConverter documentation built on March 29, 2025, 5:22 a.m.