importSpectraBruker {ASICS} | R Documentation

## Import preprocessed metabolomic spectra from Bruker files

### Description

Import preprocessed spectra from Bruker files contained in a single folder. This folder contains one subfolder for each sample. (optional) Spectra are baseline corrected, aligned and normalised by the area under the curve during the importation.

### Usage

    importSpectraBruker(
      name.dir,
      which.spectra = "first",
      ppm.grid = NULL,
      sample.names = NULL,
      ncores = 1,
      verbose = TRUE
    )

### Arguments

`name.dir` | Path of the folder containing one subfolder by sample. Each subfolder contains the Bruker files of this sample.
`which.spectra` | If there is no folder with experiment number (`all_spectra/<spectrum_name>/pdata/...`) set `which.spectra` to `NULL`. Else if there is more than one spectrum by sample (`all_spectra/<spectrum_name>/<experiment_number>/pdata/...`), which is the spectrum to import (either always the first one with `which.spectra = "first"`, always the last one with `which.spectra = "last"` or a vector of length the number of spectra that specifies the number of each spectrum to import). Default to `"first"`.
`ppm.grid` | Numeric vector of a unique grid (definition domain) for all spectra (in ppm). Default to `NULL` (in which case, the default grid of the pure library is used).
`sample.names` | Character vector of sample names. Default to `NULL` (in which case, folder names are used).
`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 spectra in columns and chemical shifts (in ppm) in rows.

### See Also

`normaliseSpectra` `alignSpectra`

### Examples

    current_path <- system.file("extdata", "example_spectra", package = "ASICS")
    spectra_data <- importSpectraBruker(current_path)

[Package ASICS version 2.3.1 Index]