README.Rmd

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output: github_document
---

# mpactr <a href="https://www.mums2.org/mpactr/"><img src="man/figures/logo.png" align="right" height="138" alt="mpactr website" /></a>

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

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## Overview

mpactr is a collection of filters for the purpose of identifying high quality MS1 features by correcting peak selection errors introduced during the pre-processing of tandem mass spectrometry data. 

Filters in this package address the following issues:

- `filter_mispicked_ions()`: removal of mispicked peaks, or those isotopic patterns that are incorrectly split during preprocessing.
- `filter_group()`: removal of features overrepresented in a specific group of samples; for example removal of features present in solvent blanks due to carryover between samples.
- `filter_cv()`: removal of non-reproducible features, or those that are inconsistent between technical replicates.
- `filter_insource_ions()`: removal of fragment ions created during the first ionization in the tandem MS/MS workflow.


All filters are independent, meaning they can be used to create a project-specific workflow, or you can learn more in [the Getting Started page](https://www.mums2.org/mpactr/articles/mpactr.html).

## Installation

You can install the CRAN version with:

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

You can install the development version of mpactr from [GitHub](https://github.com/mums2/mpactr) with:

```{r, eval = FALSE}
# install.packages("devtools")
devtools::install_github("mums2/mpactr")
```

## Get started

See the [Getting Started](https://www.mums2.org/mpactr/articles/mpactr.html) page to get started.



## Getting help

If you encounter an issue, please file an issue on [GitHub](https://github.com/mums2/mpactr/issues). Please include a minimal reproducible example with your issue.

## Contributing

Is there a feature you'd like to see included, please let us know! Pull requests are welcome on [GitHub](https://github.com/mums2/mpactr/pulls).