# Patternmatch

This is a short R pattern.search wrapper that takes in a CSV file containing
HRMS Peaks and prints all of the fragment numbers that may contain isotopes of one's
choosing (preferably halogenated compounds).

## Installation

The script has the following dependencies:
- latest version of the [Nontarget R Package](https://github.com/blosloos/nontarget) 
(This should be installed
through the devtools package)
- [purrr](https://www.rdocumentation.org/packages/purrr/versions/0.2.5)
- [enviPat](https://rdocumentation.org/packages/enviPat/versions/2.2)
- [stringr](https://www.rdocumentation.org/packages/stringr/versions/1.4.0)
- [parallel](https://www.rdocumentation.org/packages/parallel/versions/3.6.2)

Before running/configuring the script, call `make` while in the `/src`
directory or copy `script.def.R` to `script.R`.

## Additional Notes

In order to make the search run in linear time, as of right now, the entire
data table will be sorted before searching.