alignSpectra {ASICS} | R Documentation

## Alignment

### 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)

[Package ASICS version 2.3.1 Index]