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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,
  centroid = FALSE,
  hrms = FALSE
)

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.

centroid, hrms

Logical. Whether to read the centroided (MSPeak.bin) and/or profile (MSProfile.bin) mass spectra of an 'Agilent MassHunter' .d directory. Both default to FALSE, as in 'rainbow', so no mass spectra are read unless one is TRUE. Like other mass spectra, they are binned onto the m/z grid set by precision or bin_width, which coarsens high-resolution data. Ignored for the chemstation formats.

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")
} # }