ncdf4Convert-method: Method for converting CDF-3 files to CDF-4
In TargetSearch: A package for the analysis of GC-MS metabolite profiling data

Description Usage Arguments Details Value Author(s) See Also Examples

ncdf4Convert is a high level method used to convert from CDF-3 to ‘TargetSearch’ new CDF-4 custom file format.

1	ncdf4Convert(obj, path, ...)

`obj`	A `tsSample` object
`path`	A character vector representing file path in which the newly created CDF-4 files will be stored. If missing, the files will be save in the same directory as the source CDF-3 files
`...`	Extra arguments passed to `ncdf4_convert`, such as baseline correction options.

This is a high level interface to ncdf4_convert which uses a tsSample as input. The advantage of using this function is that it updates the paths to the CDF-4 files for downstream analysis.

The parameter path can be used to change the original paths, which may be necessary if those files are on a read-only file-system. If this parameter is missing, the same paths are used. Note that the path are re-cycled to match the length of the samples.

The ... can be used to pass extra arguments to ncdf4_convert and to baseline. Refer to those man pages for details.

A new tsSample object with updated CDF-4 file paths. The files are converted in the background.

Alvaro Cuadros-Inostroza

ncdf4_convert

require(TargetSearchData)
data(TSExample)
# get the CDF files
cdfpath <- file.path(find.package("TargetSearchData"), "gc-ms-data")

# update the CDF path
CDFpath(sampleDescription) <- cdfpath

# tranform the CDF (the files are copied in the current directoru)
newSamples <- ncdf4Convert(sampleDescription, path=".")