Patternmatch/specification.md

# Specifications for the script

**Use the Nontarget**

- Clusters should have large enough number of fragments (3+ maybe)
- nontarget has a pattern match function.
- Check for chlorinated compounds (has n+2, n+4, ...)

- GPL License (good)
- Script to get output for all of the results

- tabbed-deliminated text file

- Which clusters contain chlorinated compounds, how many fragments, what other
isotopes.

## format

- Readable by R.
- Manipulatable by Tidyverse
- Include it in script?

# Additional Notes

- Independent of the ordering (it might get corrupted)
- Just search for chlorinated/brominated compounds.
- Use intensity + relative abundances that `isos` shows.
- usually, use_charges will be 1
- Headers to use in script.

- Packages to do things in parallel (multiple threads)
- be able to configure the number of cores or threads used.
- make it a requirement to be tab-deliminated.

- eliminate clusters with only m/z.

# Notes

- cutint represents high enough intensity.
- mztol is in terms of ppm.
- mzfrac is in terms of absolute.
- PPM = true always

- First pass - (identify all of the fragments where chlorinated/brominated
        compounds are found and carbon)
- If isotopes exist, which ones have chlorines/bromines...
- return a data frame.

- No statistical testing required (check if it is chlorine or bromine)

- Isotopes to check (Carbon, Sulfur, Chlorine, Bromine all have n+2) (check make.isos object)

- Tweak parameters (but also put them into a slideshow/record, see how good the results are).
- **set all rules to false**

## Isotopes

- These isotopes will tend to have different intensities
- Part of the reasoning can be attributed to differences.
- Forseeable future, adapt to different isotopes.
- Capture multiple outputs of different isotopes.

## Data Summary

Per row:

- Fragment number
- Number of peaks
- top 5 (configurable) most intense m/z values.
- Averaged time output

### Derivations for above

- Fragment number - trivial
- Number of each isotope (check group counts per isotope)
- most intense - loop through the fragment and isolate. (Preserve all three categories)
- Averaged time output.

## Output num 2

- each cluster of elements, dump into a file (cluster number).


# Test Notes

- mztol seems to have a big impact on chlorine/bromine positives.