ncdf4_convert: Convert from a NetCDF file format 3 to format 4
In TargetSearch: A package for the analysis of GC-MS metabolite profiling data

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

Convert from NetCDF format 3 into a custom TargetSearch NetCDF format 4. The new NetCDF just contains the raw data in a matrix format in order to allow easier and faster data manipulation.

1 2	ncdf4_convert(cdfFile, outFile = NULL, force = FALSE, baseline = FALSE, ...)

`cdfFile`	The NetCDF file to be converted
`outFile`	The new output file. If `NULL`, it replaces the `cdfFile`'s file extension (which should be `.cdf`) by `.nc4`. If the file extension is not `.cdf`, then `.nc4` is just appended.
`force`	Logical. Set to `TRUE` to allow file overwrites, for example if the destination file still exists, in which case a warning is thrown. Default to `FALSE`.
`baseline`	Logical. Whether or not baseline correct the input file.
`...`	extra options passed to `baseline()`.

Starting from version 1.42.0, TargetSearch introduces a custom NetCDF file which is used for faster and easier data manipulation. This means, ion traces within a retention time can be quickly extracted, which if often required before plotting. Formerly, this process required parsing the whole file before the data could be extracted.

The function only takes one file at the time, to convert many files at the same time see the function ncdf4_convert_from_path() or the high level method ncdf4Convert(). Alternativelly, you can call this function in a loop or using the lapply family of functions.

Keep in mind this function is intended for internal use (or advanced users); it is exported for convenience. Using the method ncdf4Convert() is recommended.

A string. The path to the converted file or invisible.

The structure of the NetCDF format 4 is straightforward and the variables and attributes are self-evident. The following variables are defined.

retention_time is a vector representing the retention time in seconds (double).
retention_index is a vector representing the retention time indices (double). If missing, then the variable contains zeros. Its length is equal to the length of retention_time.
mass_range is vector of length two containing the minimum and maximum m/z values (integer).
intensity is matrix of intensity values (integer) where columns represent ion traces and rows are scans. The dimensions are length of "retention time" times the number of ions, ie, mass max - mass min + 1.

In addition, the following attributes are defined. Note that only creator and version are mandatory.

creator a string equal to "TargetSearch" (for indentification purposes).
version file format version (string). Currently "1.1".
time_corrected a flag (short integer) to indicate RI correction.
baseline_corrected a flag (short integer) to indicate that the file was baseline corrected by TargetSearch.

Currently, it is not possible to reconstruct the original NetCDF file from the converted file, especially if nominal mass or baseline correction was applied. On the other hand, if the NetCDF files are exported from custom chromatogram files (such as thermo raw files or LECO peg files), then the NetCDF 3 files can be deleted safely as there is always a way to recover them.

Alvaro Cuadros-Inostroza

ncdf4Convert(), ncdf4_convert_from_path(), baseline()

require(TargetSearchData)

# get files from package TargetSearchData
cdfpath <- file.path(find.package("TargetSearchData"), "gc-ms-data")

# choose any file
cdf <- file.path(cdfpath, '7235eg04.cdf')
nc4 <- '7235eg04.nc4' # save file in current path

# run the function
ret <- ncdf4_convert(cdf, nc4)

# the output should match the output file
stopifnot(ret == nc4)

# Use mapply to convert many files at the same time.
cdf <- paste0('7235eg0', 6:8, '.cdf')
nc4 <- paste0('7235eg0', 6:8, '.nc4')
ret <- mapply(ncdf4_convert, file.path(cdfpath, cdf), nc4)
stopifnot(ret == nc4)