read_shimadzu: Shimadzu ascii reader
In ethanbass/chromConverter: Chromatographic File Converter

read_shimadzu

R Documentation

Shimadzu ascii reader

Description

Reads 'Shimadzu' ascii files into R. 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
)

Arguments

`path`	Path to 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`.

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).