read_shimadzu_gcd: Shimadzu GCD parser

In ethanbass/chromConverter: Chromatographic File Converter

Shimadzu GCD parser

Description

Read chromatogram data streams from 'Shimadzu' GCD files.

Usage

read_shimadzu_gcd(
  path,
  what = "chroms",
  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 GCD file.
what	What stream to get: current options are chromatograms (chroms) and/or peak lists (peak_table). If a stream is not specified, the function will default to chroms.
format_out	Class of output. Either matrix, data.frame, or data.table.
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.

Details

A parser to read chromatogram data streams from 'Shimadzu' .gcd files. GCD files are encoded as 'Microsoft' OLE documents. The parser relies on the olefile package in Python to unpack the files. The PDA data is encoded in a stream called PDA 3D Raw Data:3D Raw Data. The GCD data stream contains a segment for each retention time, beginning with a 24-byte header.

The 24 byte header consists of the following fields:

• 4 bytes: segment label (17234).

• 4 bytes: Little-endian integer specifying the sampling interval in milliseconds.

• 4 bytes: Little-endian integer specifying the number of values in the file.

• 4 bytes: Little-endian integer specifying the total number of bytes in the file (However, this seems to be off by a few bytes?).

• 8 bytes of 00s

After the header, the data are simply encoded as 64-bit (little-endian) floating-point numbers. The retention times can be (approximately?) derived from the number of values and the sampling interval encoded in the header.

Value

A 2D chromatogram from the chromatogram stream in matrix or data.frame 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.

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.