Read CDF

Reads 'Analytical Data Interchange' (ANDI) netCDF (.cdf) files.

Usage

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

Arguments

path

Path to ANDI netCDF file.

format_out

Class of output. Either matrix, data.frame, or data.table.

data_format

Whether to return data in wide or long format. "long" returns the retention time as the first column of the data.frame or matrix, while "wide" returns it as the rownames. The mass spectra of an ANDI MS file are always long, so there it applies only to the TIC.

what

For ANDI chrom files, chroms and/or peak_table. For ANDI MS files, MS1 scans (MS1) and/or the total ion chromatogram (TIC).

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.

...

Additional arguments to the parser. For ANDI MS files, pass ms_format to return the mass spectra as a data.frame (the default) or a list.

Value

A chromatogram in the format specified by the format_out and data_format arguments.

Details

Retention times are returned in minutes, converted from the unit the file declares. An ANDI chrom file declares it in its retention_unit attribute, which also governs the peak table. Seconds is both what the template uses and what all but one of its conformance files declare, so a file that declares no unit is read as seconds, unless chromConverter wrote it, in which case it is read as minutes.

An ANDI MS file has no mandatory unit attribute, since the specification never formally defined its axes units, so scan_acquisition_time is read as seconds, the only unit the specification suggests, unless a raw_data_time_units attribute says otherwise.

Either kind of file warns about a unit it does not recognize and reads it as seconds.

Author

Ethan Bass

Examples

if (FALSE) { # \dontrun{
read_cdf("path/to/file.cdf")
} # }