binning: Binning/Bucketing of NMR spectra

In GaelleLefort/ASICS: Automatic Statistical Identification in Complex Spectra

Description

Apply a binning function on a spectrum.

Usage

binning(
  spectra,
  bin = 0.01,
  exclusion.areas = matrix(c(4.5, 5.1), ncol = 2),
  normalisation = TRUE,
  low.lim = 0.5,
  high.lim = 10,
  ncores = 1,
  verbose = TRUE,
  ...
)

Arguments

spectra	Data frame with spectra in columns and chemical shifts in rows. Colnames of this data frame correspond to sample names and rownames to chemical shift grid (in ppm).
bin	Numeric value specifying the bin width.
exclusion.areas	Definition domain of spectra that have to be excluded of the analysis (ppm). By default, the water region is excluded (4.5-5.1 ppm).
normalisation	Logical. If TRUE a normalisation is applied for each spectrum (see normaliseSpectra for details). Default to TRUE.
low.lim, high.lim	low and high chemical shift limits for the output bins (default values : low.lim = 0.5 and high.lim = 10).
ncores	Number of cores used in parallel evaluation. Default to 1.
verbose	A boolean value to allow print out process information.
...	Further arguments to be passed to the function normaliseSpectra

Value

A data frame with normalised spectra in columns and buckets in rows (bucket names correspond to the center of the bucket).

Examples

current_path <- system.file("extdata", package = "ASICS")
spectra_data <- importSpectra(name.dir = current_path,
                     name.file = "spectra_example.txt", type.import = "txt")
spectra_bin <- binning(spectra_data, bin = 0.01, type.norm = "pqn")

GaelleLefort/ASICS documentation built on July 19, 2020, 2:08 p.m.