---
title: "metaboData"
author: Jasen Finch
output: 
    prettydoc::html_pretty:
        highlight: github
        theme: tactile
vignette: >
  %\VignetteIndexEntry{metaboData}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = FALSE
)
```

metaboData provides raw and processed example metabolomics data sets.
This document concisely outlines how to access the data sets and the meta information provided. 

## Accessing data sets

Load the library:

```{r}
library(metaboData)
```

The example data sets are stored remotely in the releases of the GitHub [repository](https://github.com/aberHRML/metaboData/releases) and accessed using the [piggyback](https://docs.ropensci.org/piggyback/) package.
The available data sets can be viewed using:

```{r}
availableDataSets()
```

The available metabolomic techniques can be returned using:

```{r}
techniques()
```

The available data sets for a given metabolomic technique can be returned using:

```{r}
dataSets(techniques()[1])
```

A particular data set can be downloaded for use with:

```{r}
downloadDataSet(techniques()[1],
                dataSets()[1])
```

By default these will be stored within the library location.
This behaviour can be adjusted using the `dataSetDir` and `internalDir` arguments.

File paths for data files within a given data set can be returned using the following:

```{r}
files <- filePaths(
    techniques()[1],
    dataSets(techniques()[1])[1])
```

An experimental description can be retrieved for a given experiment of a given metabolomic technique using:

```{r}
experimentDescription <- description(
   techniques()[1],
   dataSets(techniques()[1])[1])
```

Run information can be retrieved for a given experiment of a given metabolomic technique using:

```{r}
info <- runinfo(
    techniques()[1],
    dataSets(techniques()[1])[1])

head(info)
```

For `filePaths`, `description` and `runinfo`, if the specified data set is not available locally, by default the user will be prompted to consent to downloading the data.
The `ask = FALSE` argument can be used to override this behaviour. 

The `abr1` FIE-MS data set from the [FIEmspro](https://github.com/aberHRML/FIEmspro) package is also available via lazy-load.