read_shimadzu: Read 'Shimadzu' ASCII

Description

Reads 'Shimadzu' ASCII (.txt) files. These files can be exported from 'Shimadzu LabSolutions' by right clicking on samples in the sample list and selecting File Conversion:Convert to ASCII.

Usage

read_shimadzu(
  path,
  what = "chroms",
  format_in = NULL,
  include = c("fid", "lc", "dad", "uv", "tic"),
  format_out = c("matrix", "data.frame"),
  data_format = c("wide", "long"),
  peaktable_format = c("chromatographr", "original"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  ms_format = c("data.frame", "list"),
  collapse = TRUE,
  scale = TRUE
)

Value

A nested list of elements from the specified file, where the top levels are chromatograms, peak tables, and/or mass spectra according to the value of what. Chromatograms are returned in the format specified by format_out (retention time x wavelength).

Arguments

path: Path to Shimadzu .txt ASCII file.
what: Whether to extract chromatograms (chroms), peak_table, and/or ms_spectra. Accepts multiple arguments.
format_in: This argument is deprecated and is no longer required.
include: Which chromatograms to include. Options are fid, dad, uv, tic, and status.
format_out: R format. Either matrix or data.frame.
data_format: Whether to return data in wide or long format.
peaktable_format: Whether to return peak tables in chromatographr or original format.
read_metadata: Whether to read metadata from file.
metadata_format: Format to output metadata. Either chromconverter or raw.
ms_format: Whether to return mass spectral data as a (long) data.frame or a list.
collapse: Logical. Whether to collapse lists that only contain a single element.
scale: Whether to scale the data by the scaling factor present in the file. Defaults to TRUE.

Author

Ethan Bass

Examples

Run this code

if (FALSE) { # interactive()
path <- "tests/testthat/testdata/ladder.txt"
read_shimadzu(path)
}