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Parse Agilent or Waters files with rainbow parser

Source: R/call_rainbow.R
call_rainbow.Rd

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(
  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

Ethan Bass