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# System prepended metadata

title: Code to standardize
tags: [Resources]

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tags: Resources
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# Code to standardize


| Name  | Function         | What does it do                                                           |
| ----- | ---------------- | ------------------------------------------------------------------------- |
| Elise | Extract_RamClust | Extract features from each cluster, select the one with highest intensity 
Elise   | Plot_EIC |For each feature, the EIC is plotted for each sample
Anton |FolderMZML|Converts all .d-files in a folder into mzML files
Anton |calcAdductMass|Function calculating adduct mass based on exact neutral mass
Anton & Olle|inclusionListGen|Function for automatically creating targeted analysis inclusion lists
Yan|onehotencoding|Convert factor variables to n 01 variables (n is number of levels) and convert data frame to matrix
Calle | mzCalc | Calculate "usual suspects" for different ions/adducts in pos/neg ionization from a monoisotopic mass as input
Calle | extractFeats (CRC) | Find and extract the feature in a peak table closest in mz to your specified target
Calle | getCoelutes (CRC) | find features coeluting with your target feature
Calle | eAdjust (CRC) | convenience function to calculate energy-adjusted variables using either density or residual method
Calle | findSet (CRC) | Identify the minimal set of samples covering your features of interest (useful for determining samples for targeted MSMS)
Calle | extractFeatures (CRC) | Extract instrument features from RAMClust features (could be same/similar as Elise's above)


# Recommended functions
| Package/Function | Version | What does it do | Who recommends | Date | 
| ---------------- | ------- | --------------- | -------------- | ---- |
|VennDiagram | 1.7.0  | making Venn Diagram (check Calle's StatTools package in GitLab) | Stef  | 2021-11-18
|caret  | 	6.0-90  | tuning alpha and lambda for elastic net (hasn't been tested)| Stef | 2021-11-18

Suggestions for combinations of scripts:
- FindSet + inclusionListGen (Anton)
- calcAdductMass + mzCalc (Anton)
- Extract_RamClust + extractFeatures (Elise)