alignSpectra: Alignment

In ASICS: Automatic Statistical Identification in Complex Spectra

Description

Align spectra of a data frame by a method based on the CluPA algorithm (Vu et al., (2011))

Usage

alignSpectra(
  spectra,
  reference = NULL,
  max.shift = 0.02,
  ncores = 1,
  verbose = TRUE
)

Arguments

spectra	Data frame with spectra in columns and chemical shift in rows. Colnames of this data frame correspond to pure metabolite names and rownames to chemical shift grid (in ppm).
reference	Index of the reference spectrum used for the alignment. Default to NULL, i.e. the reference spectrum is automatically detected.
max.shift	Maximum shift allowed for the alignment. Default to 0.002.
ncores	Number of cores used in parallel evaluation. Default to 1.
verbose	A boolean value to allow print out process information.

Value

A data frame with aligned spectra in columns and chemical shifts (in ppm) in rows.

References

Vu, T. N., Valkenborg, D., Smets, K., Verwaest, K. A., Dommisse, R., Lemiere, F., ... & Laukens, K. (2011). An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics, 12(1), 405.

Examples

current_path <- system.file("extdata", package = "ASICS")
spectra_data <- importSpectra(name.dir = current_path,
                     name.file = "spectra_example.txt", type.import = "txt")
spectra_align <- alignSpectra(spectra_data)

ASICS documentation built on Nov. 8, 2020, 8:19 p.m.