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Read 'Shimadzu' QGD files

Source: R/read_shimadzu_qgd.R
read_shimadzu_qgd.Rd

Reads 'Shimadzu GCMSsolution' .qgd GC-MS data files.

Usage

read_shimadzu_qgd(
  path,
  what = c("MS1", "TIC"),
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  collapse = TRUE
)

Arguments

path

Path to 'Shimadzu' .qgd file.

what

What stream to get: current options are MS1 and/or TIC. If a stream is not specified, the function will return both streams.

format_out

Matrix or data.frame.

data_format

Either wide (default) or long.

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. Defaults to TRUE.

Value

A 2D chromatogram from the chromatogram stream in matrix, data.frame, or data.table format, according to the value of format_out. The chromatograms will be returned in wide or long format according to the value of data_format.

A chromatogram or list of chromatograms in the format specified by data_format and format_out. If data_format is wide, the chromatogram(s) will be returned with retention times as rows and a single column for the intensity. If long format is requested, two columns will be returned: one for the retention time and one for the intensity. The format_out argument determines whether chromatograms are returned as a matrix, data.frame, or data.table. Metadata can be attached to the chromatogram as attributes if read_metadata is TRUE.

Details

The MS data is stored in the "GCMS Raw Data" storage, which contains a MS Raw Data stream with MS scans, a TIC Data stream containing the total ion chromatogram, and a Retention Time stream containing the retention times. All known values are little-endian. The retention time stream is a simple array of 4-byte integers. The TIC stream is a simple array of 8-byte integers corresponding to retention times stored in the retention time stream. The MS Raw Data stream is blocked by retention time. Each block begins with a header consisting of the following elements:

  • scan number (4-byte integer)

  • retention time (4-byte integer)

  • unknown (12-bytes)

  • number of bytes in intensity values (2-byte integer)

  • unknown (8-bytes)

After the header, the rest of the block consists of an array of mz values and intensities. The mz values are encoded as 2-byte integers where each mz value is scaled by a factor of 20. Intensities are encoded as (unsigned) integers with variable byte-length defined by the value in the header.

Note

This parser is experimental and may still need some work. It is not yet able to interpret much metadata from the files.

See also

Other 'Shimadzu' parsers: read_shimadzu(), read_shimadzu_gcd(), read_shimadzu_lcd(), read_sz_lcd_2d(), read_sz_lcd_3d()

Author

Ethan Bass