doProcessing
doProcessing is the main function of this package. Indeed, this function performs
the complete processing of a set of 1D NMR spectra from the FID (raw data) and based on a
processing sequence (macro-command file). An additional file specifies all the spectra to
be considered by associating their sample code as well as the levels of experimental
factors to which they belong. In this way it is possible to select only a subset of spectra
instead of the whole set.
doProcessing(path, cmdfile, samplefile = NULL, bucketfile = NULL, ncpu = 1)
path |
The full path of either the raw spectra directory on the disk |
cmdfile |
The full path name of the Macro-commands file for processing (text format) |
samplefile |
The full path name of the Sample file (tabular format) |
bucketfile |
The full path name of the file of bucket's zones (tabular format) |
ncpu |
The number of cores [default: 1] |
doProcessing returns a list containing the following components:
samples : the samples matrix with the correspondence of the raw spectra,
as well as the levels of the experimental factors if specified in the input.
factors : the factors matrix with the corresponding factor names.
At minimum, the list contains the Samplecode label corresponding to the samples without their
group level.
rawids : list of the full directories of the raw spectra (i.e. where the FID files
are accessible)
infos : list of the acquisition and processing parameters for each (raw) spectra.
specMat : objects list regarding the spectra data.
int : the matrix of the spectra data (nspec rows X size
columns)
nspec : the number of spectra
size : the size (i.e number of points) of each spectra
ppm_min, ppm_max : the minimum and the maximum ppm values of
spectra
ppm : the vector of the ppm values (size values)
dppm : the ppm increment between each point
buckets_zones : the matrix of the buckets zones including two columns
(min and max)
namesASintMax : boolean - If TRUE, generate all output matrix with
bucket names based on ppm values of the maximum of the average intensity of all spectra within
the ppm range of each bucket. If FALSE (default), then bucket names will be based on the ppm
range center of each bucket.
the NMRProcFlow online documentation https://nmrprocflow.org/ and especially the Macro-command Reference Guide (https://nmrprocflow.org/themes/pdf/Macrocommand.pdf)
data_dir <- system.file("extra", package = "Rnmr1D")
cmdfile <- file.path(data_dir, "NP_macro_cmd.txt")
samplefile <- file.path(data_dir, "Samples.txt")
out <- Rnmr1D::doProcessing(data_dir, cmdfile=cmdfile,
samplefile=samplefile, ncpu=detectCores())Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.