ASICS {ASICS} | R Documentation

## Automatic Statistical Identification in Complex Spectra

### Description

Quantification of 1D 1H NMR spectra with ASICS method using a library of pure metabolite spectra. The method is presented in Tardivel et al. (2017).

### Usage

    ASICS(spectra_obj, exclusion.areas = matrix(c(4.5, 5.1), ncol = 2),
      max.shift = 0.02, pure.library = NULL, threshold.noise = 0.02,
      combine = TRUE, seed = 1234, ncores = 1, verbose = TRUE)

### Arguments

`spectra_obj` | An object of class Spectra obtained with the function createSpectra.
`exclusion.areas` | Definition domain of spectra that has to be excluded for the quantification (ppm). By default, the water region is excluded (4.5-5.1 ppm).
`max.shift` | Maximum chemical shift allowed (in ppm). Default to 0.02.
`pure.library` | An object of class PureLibrary containing the reference spectra (pure metabolite spectra). If `NULL`, the library included in the package (that contains 191 reference spectra) is used.
`threshold.noise` | Threshold for signal noise. Default to 0.02.
`combine` | Logical. If `TRUE`, information from all spectra are taken into account to align individual library.
`seed` | Random seed to control randomness in the algorithm (used in the estimation of the significativity of a given metabolite concentration).
`ncores` | Number of cores used in parallel evaluation. Default to `1`.
`verbose` | A boolean value to allow print out process information.

### Value

An object of type ASICSResults containing the quantification results.

### References

Tardivel P., Canlet C., Lefort G., Tremblay-Franco M., Debrauwer L., Concordet D., Servien R. (2017). ASICS: an automatic method for identification and quantification of metabolites in complex 1D 1H NMR spectra. Metabolomics, 13(10): 109. https://doi.org/10.1007/s11306-017-1244-5

### See Also

ASICSResults `pure_library` `createSpectra`

### Examples

    # Import data and create object
    current_path <- system.file("extdata", package = "ASICS")
    spectra_data <- importSpectra(name.dir = current_path,
                         name.file = "spectra_example.txt", type.import = "txt")
    spectra_obj <- createSpectra(spectra_data)

    # Estimation of relative quantification of Lactate and L-Alanine
    to_exclude <- matrix(c(4.5, 10), ncol = 2)
    pure_lib <- pure_library[getSampleName(pure_library) %in%
                             c("Lactate", "L-Alanine")]
    resASICS <- ASICS(spectra_obj[1], exclusion.areas = to_exclude,
                      pure.library = pure_lib, combine = FALSE)

[Package ASICS version 2.2.0 Index]