---
title: "Core Utils for Metabolomics Data"
package: MetaboCoreUtils
output:
  BiocStyle::html_document:
    toc_float: true
vignette: >
  %\VignetteIndexEntry{Core Utils for Metabolomics Data}
  %\VignetteEngine{knitr::rmarkdown}
  %%\VignetteKeywords{Mass Spectrometry, MS, MSMS, Metabolomics, Infrastructure, Quantitative }
  %\VignetteEncoding{UTF-8}
---

```{r style, echo = FALSE, results = 'asis'}
BiocStyle::markdown()
```

**Package**: `r BiocStyle::Biocpkg("MetaboCoreUtils")`<br />
**Authors**: `r packageDescription("MetaboCoreUtils")[["Author"]] `<br />
**Last modified:** `r file.info("MetaboCoreUtils.Rmd")$mtime`<br />
**Compiled**: `r date()`

# Introduction

The `MetaboCoreUtils` defines metabolomics-related core functionality provided
as low-level functions to allow a data structure-independent usage across
various R packages. This includes functions to calculate between ion (adduct)
and compound mass-to-charge ratios and masses or functions to work with chemical
formulas. The package provides also a set of adduct definitions and information
on some commercially available internal standard mixes commonly used in MS
experiments.

For a full list of function, see

```{r, message = FALSE}
library("MetaboCoreUtils")
ls(pos = "package:MetaboCoreUtils")
```

or the [reference
page](https://rformassspectrometry.github.io/MetaboCoreUtils/reference/index.html)
on the package webpage.


# Installation

The package can be installed with the `BiocManager` package. To
install `BiocManager` use `install.packages("BiocManager")` and, after that,
`BiocManager::install("MetaboCoreUtils")` to install this package.


# Examples

The functions defined in this package utilise basic classes with the
aim of being reused in packages that provide a more formal, high-level
interface.

The examples below demonstrate the basic usage of the functions from the
package.

```{r}
library(MetaboCoreUtils)
```


## Conversion between ion m/z and compound masses

The `mass2mz` and `mz2mass` functions allow to convert between compound masses
and ion (adduct) mass-to-charge ratios (m/z). The `MetaboCoreUtils` package
provides definitions of common ion adducts generated by electrospray ionization
(ESI). These can be listed with the `adductNames` function.

```{r}
adductNames()
```

With that we can use the `mass2mz` function to calculate the m/z for a set of
compounds assuming the generation of certain ions. In the example below we
define masses for some theoretical compounds and calculate their expected m/z
assuming that ions `"[M+H]+"` and `"[M+Na]+"` are generated.

```{r}
masses <- c(123, 842, 324)
mass2mz(masses, adduct = c("[M+H]+", "[M+Na]+"))
```

As a result we get a `matrix` with each row representing one compound and each
column the m/z for one of the defined adducts. With the `mz2mass` we could
perform the reverse calculation, i.e. from m/z to compound masses.


## Working with chemical formulas

The lack of consistency in the format in which chemical formulas are written
poses a big problem comparing formulas coming from different resources. The
`MetaboCoreUtils` package provides functions to *standardize* formulas as well
as combine formulas or substract elements from formulas. Below we use an
artificial example to show this functionality. First we standardize a chemical
formula with the `standardizeFormula` function.

```{r}
frml <- "Na3C4"
frml <- standardizeFormula(frml)
frml
```

Next we add `"H2O"` to the formula using the `addElements` function.

```{r}
frml <- addElements(frml, "H2O")
frml
```

We can also substract elements with the `subtractElements` function:

```{r}
frml <- subtractElements(frml, "H")
frml
```

The counts for individual elements in a chemical formula can be calculated with
the `countElements` function.

```{r}
countElements(frml)
```


# Contributions

If you would like to contribute any low-level functionality, please
[open a GitHub
issue](https://github.com/RforMassSpectrometry/MetaboCoreUtils/issues) to
discuss it. Please note that any
[contributions](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/RforMassSpectrometry.html#contributions)
should follow the [style
guide](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/RforMassSpectrometry.html#coding-style)
and will require an appropriate unit test.


If you wish to reuse any functions in this package, please just go
ahead. If you would like any advice or seek help, please either [open
a GitHub
issue](https://github.com/RforMassSpectrometry/MetaboCoreUtils/issues).


# Session information {-}

```{r sessioninfo, echo=FALSE}
sessionInfo()
```