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Write a chromatogram matrix as an ANDI-MS CDF file

Source: R/GCMS_cdf.R
write_GCMS_cdf.Rd

Export scan-by-mass intensities for GCMSdeco() or external GC/MS software. The NetCDF classic file includes scan indexing, total ion counts, mass ranges and ANDI-MS administrative and instrument records.

Usage

write_GCMS_cdf(
  y,
  cdf_file,
  time = as.numeric(rownames(y)),
  mass = as.numeric(colnames(y)),
  sample_name = tools::file_path_sans_ext(basename(cdf_file))
)

Arguments

y

Finite nonnegative numeric matrix, with scans in rows and nominal mass channels in columns. Zero channels are retained.

cdf_file

Output .cdf path.

time

Increasing scan times in minutes. Defaults to numeric row names.

mass

Increasing nonnegative integer m/z values. Defaults to numeric column names.

sample_name

Sample identity recorded in the header; defaults to the output filename without its extension.

Value

Invisibly, the normalized output path.

Details

Intensities are stored without rescaling or rounding. Integer data fitting in a signed 32-bit integer use ANDI Long storage; other data use Double. Scan times are converted to seconds in the file. Every channel is written in every scan, including exact zeros. The file's timestamp records export time; acquisition metadata are left unspecified.

See also

GCMSdeco(), splogconNMF()

Examples

# \donttest{
if (requireNamespace("ncdf4", quietly = TRUE)) {
  data(GCMS_data1)
  cdf <- tempfile(fileext = ".cdf")
  write_GCMS_cdf(GCMS_data1, cdf)
  unlink(cdf)
}
# }