README.Rmd

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output: github_document
---

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```{r, include = FALSE}
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# isoorbi <a href='https://isoorbi.isoverse.org/'> <img src="inst/www/logo.png" align="right" height="138" /> </a>

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## Overview

The goal of the isoorbi R package is to help you process isotopocule measurements from an **Orbitrap Isotope Solutions** mass spectrometer. It expects <code>.isox</code> files created by IsoX as input.

## Installation

You can install the current CRAN version of `isoorbi` with:

```{r, eval = FALSE}
install.packages("isoorbi")
```

To use the latest updates, you can install the development version of `isoorbi` from [GitHub](https://github.com/) with:

```{r, eval = FALSE}
if(!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
devtools::install_github("isoverse/isoorbi")
```

## Show me some code

```{r "example"}
library(isoorbi)

system.file(package = "isoorbi", "extdata", "testfile_flow.isox") |>
  orbi_read_isox() |>
  orbi_flag_satellite_peaks() |>
  orbi_define_basepeak(basepeak_def = "M0")|> 
  orbi_summarize_results(ratio_method = "sum") |>
  orbi_export_data_to_excel(file = "data_summary.xlsx")
```

```{r, include = FALSE}
unlink("data_summary.xlsx")
```


## Package layout

![](man/figures/figure_flowchart.png){width=60%}

## Getting help

If you encounter a bug, please file an issue with a minimal reproducible example on [GitHub](https://github.com/isoverse/isoorbi/issues). 

For questions and other discussion, please use the [isoorbi slack workspace](https://isoorbi.slack.com).