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Call 'rainbow' parsers

Source: R/call_rainbow.R
call_rainbow.Rd

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

Usage

call_rainbow(
  path,
  format_in = c("agilent_d", "waters_raw", "masshunter", "chemstation", "chemstation_uv",
    "chemstation_fid", "chemstation_ms"),
  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,
  sparse = TRUE,
  bin_width = NULL
)

Arguments

path

Path to file.

format_in

Format of the supplied files. Either agilent_d, waters_raw, masshunter, chemstation, chemstation_uv, chemstation_fid, or chemstation_ms.

format_out

Class of output. Either matrix, data.frame, or data.table.

data_format

Whether to return data in wide (default) or long format.

by

How to group the returned list: by detector (default), or by name, one element per data file in the directory.

what

Which detectors to return (e.g. MS, UV, CAD, ELSD). Applies only when by = "detector". Defaults to NULL, which returns all of them.

read_metadata

Logical. Whether to attach metadata. Defaults to TRUE.

metadata_format

Format to output metadata. Either chromconverter (standardized field names) or raw (vendor field names, unmapped).

collapse

Logical. Whether to collapse lists that only contain a single element. Defaults to TRUE.

precision

Number of decimals of the m/z grid, which is spaced 10^-precision apart. Defaults to 1. Ignored if bin_width is supplied.

sparse

Logical. Whether to drop zero intensities from MS data. Applies only to long format. Defaults to TRUE.

bin_width

Width of the m/z grid, in daltons. An alternative to precision for grids that are not a power of ten (e.g. 0.5). Defaults to NULL, in which case the grid is derived from precision as 10^-precision.

Value

A (nested) list of chromatograms, or a single chromatogram for the chemstation formats, in the class given by format_out. The list is grouped according to the value of by.

Details

Uses rainbow parsers to read in Agilent (.D) and Waters (.raw) files. For agilent_d, waters_raw and masshunter, path is the data directory (.D or .raw), and the result is a list grouped according to by. For the chemstation formats, path is a single file (e.g. .uv), the result is a single chromatogram, and by and what are ignored. Otherwise, data can be filtered by detector type using the what argument.

See also

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

Author

Ethan Bass

Examples

if (FALSE) { # \dontrun{
call_rainbow("path/to/file.D", format_in = "agilent_d")
} # }