call_rainbow: Call 'rainbow' parsers Parse 'Agilent' or 'Waters' files with...

In ethanbass/chromConverter: Chromatographic File Converter

Call 'rainbow' parsers Parse 'Agilent' or 'Waters' files with rainbow parsers

Description

Uses rainbow parsers to read in Agilent (.D) and Waters (.raw) files. If format_in is "agilent_d" or "waters_raw", a directory of the appropriate format (.d or .raw) should be provided to the file argument. If format_in is "chemstation_uv" a .uv file should be provided. Data can be filtered by detector type using the what argument.

Usage

call_rainbow(
  path,
  format_in = c("agilent_d", "waters_raw", "masshunter", "chemstation", "chemstation_uv",
    "chemstation_fid"),
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  by = c("detector", "name"),
  what = NULL,
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  collapse = TRUE,
  precision = 1
)

Arguments

path	Path to file
format_in	Format of the supplied files. Either agilent_d, waters_raw, or chemstation.
format_out	R format. Either matrix, data.frame, or data.table.
data_format	Whether to return data in wide or long format.
by	How to order the list that is returned. Either detector (default) or name.
what	What types of data to return (e.g. MS, UV, CAD, ELSD). This argument only applies if by == "detector".
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.
precision	Number of decimals to round mz values. Defaults to 1.

Value

Returns a (nested) list of matrices or data.frames according to the value of format_out. Data is ordered according to the value of by.

Author(s)

Ethan Bass

See Also

Other external parsers: call_entab(), call_openchrom(), read_thermoraw(), sp_converter(), uv_converter()

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