A short script to use the nontarget pattern.match function to print useful information about clusters.
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# Patternmatch
This is a short R pattern.search wrapper that takes in a CSV file containingHRMS Peaks and prints all of the fragment numbers that may contain isotopes of one'schoosing (preferably halogenated compounds).
## Installation
The script uses the following packages:
- latest version of the [Nontarget R Package](https://github.com/blosloos/nontarget) (It is recommended to install this package through the devtools package)- [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 simply copy `/src/script.def.R` to `/src/script.R`.
## Configuration
All configuration variables are located at the top of the script.
## Output
The script should print a list with data for all clusters that contain theisotopes to be searched for.
If `verbose.enable` is set to `TRUE`, files of the form `(fragment number).txt`containing the `pattern.search` output will be printed to the directoryspecified in `verbose.outputdir`, assuming the directory already exists.
## Additional Notes
As windows does not allow forking, the number of cores used on it will beconstrained to 1.
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