__  __      _        _           _ _ _               _____ _                            
 |  \/  |    | |      | |         | (_) |             / ____| |                           
 | \  / | ___| |_ __ _| |__   ___ | |_| |_ ___  ___  | |    | | ___  __ _ _ __   ___ _ __ 
 | |\/| |/ _ \ __/ _` | '_ \ / _ \| | | __/ _ \/ __| | |    | |/ _ \/ _` | '_ \ / _ \ '__|
 | |  | |  __/ || (_| | |_) | (_) | | | ||  __/\__ \ | |____| |  __/ (_| | | | |  __/ |   
 |_|  |_|\___|\__\__,_|_.__/ \___/|_|_|\__\___||___/  \_____|_|\___|\__,_|_| |_|\___|_|   

Metabolites Cleaner

Metabolites Cleaner is a tool to tidy up compounds list to simplify further metabolomics analysis

NIST Cleaner

Removes Targert and Orthogonal as well as removes metabolites found in the folder Rejected from the NIST.txt file. Provides detailed info of the processing done.

Excel Cleaner

Reject unwanted metabolites from the Excel workbook. Creates a worksheet with rejected metabolites.

Name Fixer

Cleans metabolite names in the excel table.

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How to run?

1. Compatible with Windows command prompt. Just double click Metabolites Cleaner.bat to run.
2. It automatically checks if R is installed and finds correct path to it. If not R found then it downloads and installs one.

Note! By default it requires installed R in C'\Program Files\R... directory.

3. It automatically downloads and installs all required R packages.
4. Select an option to run

Note! Make sure Metabolites Cleaner folder and working folder with input files are in folders named with no special characters and spaces. Avoid use spaces. Use _ (underline) instead.

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How to use NIST Cleaner?

1. Navigate to the png files repository of the metabolites peaks.
2. Create Rejected folder in the root of the png files repository.
3. All png files you want to discard move to Rejected folder.
4. Select RDA_Target_NIST.txt file.
5. By default it removes Targert, Orthogonal and entries found in Rejected folder. Modify config.yml. To activate function set 1 to a property, to deactivate set 0.

remove_Target: 1
remove_Orthogonal: 1
remove_Recursion: 0
remove_rejceted: 1

How NIST Cleaner work?

1. Creates RDA_Target_NIST_CLEAN.txt file in the root folder.
2. Removes selected entry types.
3. Finds matches of the png names in the Rejected folder in the NIST file and removes such entries.
4. Finds exceptions and ignores errors so it will ends properly.
5. Provides detailed info about the processions was done.

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How to use Excel Cleaner?

1. Navigate to the png files repository of the metabolites peaks.
2. Create Rejected folder (if such does not exist) in the root folder.
3. All png files you want ot discard move to Rejected folder.
4. Select excel file. Excel Cleaner by default uses worksheet Integrated Unimodal 1. You can modify it in config.yml file following variable:

xlsx_sheet: Integrated Unimodal 1

5. In config.yml select search algorithm to use, where search by index set 0, search by name set 1:

search_algorithm: 1

6. Select input file with pop up window.

How Excel Cleaner work?

1. Metabolites Cleaner creates RDA_Target_Data_Model_CLEAN.xlsx file that is a duplicate file RDA_Target_Data_Model.xlsx.
2. In the RDA_Target_Data_Model_CLEAN.xlsx worksheet Integrated Unimodal 1 moves all columns of metabolites that found in Rejected folder to Rejected worksheet.
3. Duplicates worksheet clean Integrated Unimodal 1 and names it CLEAN NAMES.
4. Worksheet CLEAN NAMES cleans all head names of columns with metabolites.

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How to use Name Fixer?

1. Select excel file to fix component names.
2. Done. By default it uses worksheet Integrated Unimodal 1. You can modify it in config.yml file following variable:

xlsx_sheet: Integrated Unimodal 1

How Name Fixer work?

1. Removes index if such exists: S227_GLUCOSE_6_PHOSPHATE_MEOX_6TMS_minor___2 -> _GLUCOSE_6_PHOSPHATE_MEOX_6TMS_minor___2.
2. Removes nTMS, where n is n character and digit and characters followed after nTMS: _GLUCOSE_6_PHOSPHATE_MEOX_6TMS_minor___2 -> _GLUCOSE_6_PHOSPHATE_MEOX_.
3. Removes MEOX and characters followed after MEOX: _GLUCOSE_6_PHOSPHATE_MEOX_ -> _GLUCOSE_6_PHOSPHATE_.
4. Removes unwanted characters such as spaces and underlines: _GLUCOSE_6_PHOSPHATE_ -> GLUCOSE 6 PHOSPHATE.
5. Replaces uppercase to lowercase: GLUCOSE 6 PHOSPHATE -> Glucose 6 phosphate.

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Metabolites Cleaner tool requires listed below open source CRAN packages:

dplyr
readxl
yaml
rio
openxlsx
progress
R.utils
stringdist
yaml
stringr

Note! Run \res\OS_environment.bat to switch OS_environment key to run Metabolites Cleaner in Windows terminal.