---
title: "Automatic Statistical Identification in Complex Spectra (ASICS)"
author: "Gaëlle Lefort, Rémi Servien and Nathalie Vialaneix"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
package: ASICS
vignette: >
  %\VignetteIndexEntry{ASICS}
  %\VignetteEncoding{UTF-8}
  %\VignetteEngine{knitr::rmarkdown}
editor_options: 
  chunk_output_type: console
---

## Package description 
The **R** package `ASICS` is a fully automated procedure to identify and 
quantify metabolites in $^1$H 1D-NMR spectra of biological mixtures 
(Tardivel *et al.*, 2017). It will enable empowering NMR-based metabolomics by 
quickly and accurately helping experts to obtain metabolic profiles. In addition
to the quantification method, several functions allowing spectrum 
preprocessing or statistical analyses of quantified metabolites are available.

The full ASICS User's Guide is available after installing the package. It can be
opened with:

```{r userguide, warning=FALSE}
library(ASICS)
ASICSUsersGuide(view = FALSE)
```

## Quick overview of main functions

Data are imported in a data frame from Bruker files with the 
`importSpectraBruker` function.
```{r data_import, results='hide'}
current_path <- system.file("extdata", "example_spectra", package = "ASICS")
spectra_data <- importSpectraBruker(current_path)
```

Then, from the data frame, a `Spectra` object is created. This is a required 
step for the quantification.
```{r create_spectra, results='hide'}
spectra_obj <- createSpectra(spectra_data)
```

Identification and quantification of metabolites can now be carried out using 
only the function `ASICS`. For this example, only two metabolites are kept 
(Alanine and Lactate) and quantification is performed on the first spectra.
```{r quantification}
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, verbose = FALSE)
```

Some analysis functions can be carried out on the quantification results. More
details can be found in the user's guide with the use of a real dataset.

## 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

