Reads 'Analytical Data Interchange' (ANDI) netCDF (.cdf) files.
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,
...
)A chromatogram in the format specified by the format_out and
data_format arguments.
Path to ANDI netCDF file.
Class of output. Either matrix, data.frame,
or data.table.
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.
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).
Whether to read metadata from file.
Format to output metadata. Either chromconverter
or raw.
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.
Ethan Bass