read_shimadzu_qgd: Read 'Shimadzu' QGD

In ethanbass/chromConverter: Chromatographic File Converter

Read 'Shimadzu' QGD

Description

Parser for 'Shimadzu GCMSsolution' .qgd 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.
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.

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.

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.

Note

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

Author(s)

Ethan Bass

ethanbass/chromConverter documentation built on Jan. 14, 2025, 2:11 a.m.