alignment {ASICS}R Documentation

Alignment

Description

Align spectra of a data frame with the CluPA algorithm (Vu et al., (2011))

Usage

alignment(spectra, baseline.threshold = 0.02, reference = NULL,
  max.shift = 0.002)

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).

baseline.threshold

Value of baseline threshold used to identify peaks. Default to 0.02.

reference

Index of the reference spectrum used for the alignment. Default to NULL, i.e. the reference spectrum is automatically detected with the findRef function of the speaq package.

max.shift

Maximum shift allowed for the alignment. Default to 0.002.

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 <- file.path(system.file("extdata", package = "ASICS"),
                          "spectra_example.txt")
spectra_data <- read.table(current_path, header = TRUE, row.names = 1)
spectra_base_cor <- alignment(spectra_data)

[Package ASICS version 1.2.0 Index]