Read files from 'Agilent ChemStation' .D directories

Reads files from 'Agilent' .D directories.

Usage

read_agilent_d(
  path,
  what = c("dad", "chroms", "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 'Agilent' .D directory.

what

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

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 or raw.

collapse

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

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.

Details

Currently this function is limited to reading .uv, .ch and peak_table elements.

See also

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

Author

Ethan Bass

Examples

if (FALSE) { # interactive()
read_agilent_d("tests/testthat/testdata/RUTIN2.D")
}