Parse Agilent or Waters files with rainbow parser — call

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

Arguments

file: Path to file
format_in: Format of the supplied files. Either agilent_d, waters_raw, or chemstation.
format_out: R format. Either matrix or data.frame.
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.
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

Ethan Bass