read_cdf: Read CDF file
In ethanbass/chromConverter: Chromatographic File Converter

read_cdf

R Documentation

Read CDF file

Description

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`.