ncdf4_convert_from_path: Convert CDF files to CDF4 from a path automatically

In acinostroza/TargetSearch: A package for the analysis of GC-MS metabolite profiling data

Convert CDF files to CDF4 from a path automatically

Description

Scan and convert NetCDF format 3 files into a custom TargetSearch NetCDF format 4 automatically. The function scans the given input path(s) for files with "cdf" extension. This function simply wraps around ncdf4_convert(), so that function will then convert each detected file.

Usage

ncdf4_convert_from_path(cdf_path = ".", out_path = cdf_path, recursive = FALSE, ignore.case = TRUE, ...)

Arguments

cdf_path	Character string. The path(s) to scan for CDF files.
out_path	Character string. The output path(s) in which the converted files will be saved.
recursive	Logical. Should the search recurse into directories?
ignore.case	Logical. Should the file extension matching be case insensitive?
...	Extra options passed to ncdf4_convert(), which in turn can be passed to baseline().

Details

This function simply searches for CDF-3 files and converts them to CDF-4 (custom format). By default the current path is scanned and files are converted and save in the same place.

Multiple input directories can be given. If this is the case, the output path out_path must be either a single path (in which case all files will be copied to the same directory) or an equal number of paths, such that there is a corresponding match between input and output directories. If not, an assertion error will be raised.

By default the search is case insensitive (see parameter ignore.case). For sensitive case matching, the function looks for all lowercase extension cdf. At the moment, it is not possible to change this pattern.

If recursive is TRUE, the search will also descend into subdirectories and the converted files will follow a similar directory structure. Output directories will be created on demand if required (this is actually done by ncdf4_convert() internally).

Value

A character vector of generated files or invisible.

Author(s)

Alvaro Cuadros-Inostroza

See Also

ncdf4_convert(), baseline()

Examples

# in this example we'll use a temporary directory as source
# and storage of CDF (because we need to reduce testing time in Bioc)

# get some files from package TargetSearchData and copy them
# to `srcdir`
require(TargetSearchData)
cdffiles <- tsd_cdffiles()[1:4]
srcdir <- file.path(tempdir(), 'gc-ms-data')
dir.create(srcdir)
file.copy(cdffiles, srcdir)

# convert to output directory set above
outdir <- tempfile()
ncdf4_convert_from_path(srcdir, outdir)

# recursive search. note that output files will be saved under "gc-ms-data"
# in the output directory
cdfpath <- tempdir() # (base path where we copy the CDF files)
ncdf4_convert_from_path(cdfpath, outdir, recursive=TRUE)

# clean-up the mess
unlink(c(srcdir, outdir), recursive=TRUE)

acinostroza/TargetSearch documentation built on Nov. 13, 2024, 12:28 a.m.