Read CDF file — read_cdf • chromConverter

Parser for Analytical Data Interchange (ANDI) netCDF 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. For 2D files, "long" format returns the retention time as the first column of the data.frame or matrix while "wide" format returns the retention time as the rownames of the object.
what: For ANDI chrom files, whether to extract chroms and/or peak_table. For ANDI ms files, whether to extract MS1 scans (MS1) or the total ion chromatogram (TIC).
read_metadata: Whether to read metadata from file.
metadata_format: Format to output metadata. Either chromconverter or raw.
collapse: Logical. Whether to collapse lists that only contain a single element.
...: Additional arguments to parser. The ms_format argument can be used here to specify whether to return mass spectra in list format or as a data.frame.

Value

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

Author

Ethan Bass