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Patternmatch
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A short script to use the nontarget pattern.match function to print useful information about clusters.
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Patternmatch/README.md

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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 uses the following packages:

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 the isotopes 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 directory specified in verbose.outputdir, assuming the directory already exists.