alignment {ASICS} | R Documentation |
Align spectra of a data frame with the CluPA algorithm (Vu et al., (2011))
alignment(spectra, baseline.threshold = 0.02, reference = NULL, max.shift = 0.002)
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 |
max.shift |
Maximum shift allowed for the alignment. Default to 0.002. |
A data frame with aligned spectra in columns and chemical shifts (in ppm) in rows.
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.
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)