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Read 'Shimadzu' GCD

Source: R/read_shimadzu_gcd.R
read_shimadzu_gcd.Rd

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 'Shimadzu' .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

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

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.

Value

A 2D chromatogram in the format specified by data_format and format_out. If data_format is wide, the chromatogram will be returned with retention times as row names 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 the chromatogram is returned as a matrix, data.frame, or data.table. Metadata are attached to the chromatogram as attributes if read_metadata is TRUE.

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 chromatogram data is encoded in streams titled LSS Raw Data:Chromatogram Ch<#>. Each stream begins with a 24-byte header:

  • 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 stream.

  • 4 bytes: Little-endian integer specifying a byte count, which does not match the size of the stream exactly.

  • 8 bytes of 00s

After the header, the data are encoded as 64-bit (little-endian) floating-point numbers. Retention times are derived from the number of values and the sampling interval encoded in the header, rather than read from the file: the nth value is placed at n times the sampling interval.

See also

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

Author

Ethan Bass

Examples

if (FALSE) { # \dontrun{
read_shimadzu_gcd("path/to/file.gcd")
} # }