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 1.0.1 Index]